Module Expr Str Import alias Import alias Import alias Import alias ImportFrom alias ImportFrom alias Import alias ImportFrom alias ImportFrom alias ImportFrom alias alias alias alias ImportFrom alias FunctionDef arguments args NameParam defaults body Return BinOpMod Str TupleLoad SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index Str decorator_list Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index Str Assign NameStore Call NameLoad NameLoad Assign NameStore ListLoad For NameStore SubscriptLoad NameLoad Index Str body AugAssignAdd NameStore Call NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str If CompareEq Call NameLoad NameLoad Num body Print Str Print Str Print Call AttributeLoad Str attr SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr Num Expr Call NameLoad SubscriptLoad NameLoad Index Str Assign NameStore ListLoad For NameStore NameLoad body Assign NameStore Call NameLoad NameLoad SubscriptLoad NameLoad Index Str NameLoad Expr Call AttributeLoad NameLoad attr NameLoad If SubscriptLoad AttributeLoad NameLoad attr Index Str body Assign NameStore Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Str Assign NameStore ListComp NameLoad comprehension NameStore Call NameLoad NameLoad CompareIn SubscriptLoad SubscriptLoad NameLoad Index Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Index Str NameLoad orelse Assign NameStore Call NameLoad NameLoad Print Str For NameStore NameLoad body Print NameLoad Print Print BinOpMod Str SubscriptLoad NameLoad Index Str Print BinOpMod Str NameLoad Print Assign NameStore SubscriptLoad NameLoad Index Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Expr Call NameLoad NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Expr Call NameLoad NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Expr Call NameLoad NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Expr Call NameLoad NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Expr Call NameLoad NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Expr Call NameLoad NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Expr Call NameLoad Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad BinOpMod Str NameLoad BinOpMod Str NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore Call NameLoad NameLoad Assign TupleStore NameStore NameStore NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index NameLoad Index Str Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index NameLoad Index Str Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index NameLoad Index Str Assign NameStore Dict Str Str Str Str NameLoad BinOpMod Str TupleLoad NameLoad NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Print BinOpMod Str TupleLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad SubscriptLoad NameLoad Index Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad BinOpMod Str NameLoad BinOpMod Str NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign NameStore ListComp NameLoad comprehension ListStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Assign NameStore Call AttributeLoad Str attr ListComp BinOpMod Str NameLoad comprehension NameStore NameLoad Print BinOpMod Str TupleLoad Call AttributeLoad Str attr ListComp Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad comprehension NameStore NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Str Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad NameLoad NameLoad decorator_list Call NameLoad Str Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Str Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad SubscriptLoad NameLoad Index Str NameLoad SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index Str NameLoad NameLoad decorator_list Call NameLoad Str Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore BinOpAdd SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Index Num Str TryExcept body Expr Call AttributeLoad NameLoad attr NameLoad handlers ExceptHandler type NameLoad name NameStore body If CompareNotEq AttributeLoad NameLoad attr Num body Raise NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore ListStore NameStore NameStore ListStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Str Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad SubscriptLoad NameLoad Index Str NameLoad NameLoad NameLoad NameLoad Expr Call NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str Call NameLoad ListLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Str Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index Str NameLoad NameLoad decorator_list Call NameLoad Str Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore ListStore NameStore NameStore ListStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Str Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad SubscriptLoad NameLoad Index Str NameLoad NameLoad NameLoad Expr Call NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str Call NameLoad ListLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameStore NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Str Print BinOpMod Str NameLoad Expr Call NameLoad Str NameLoad SubscriptLoad NameLoad Index Str NameLoad SubscriptLoad NameLoad Index Str NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad NameLoad Call NameLoad Str ListLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameStore NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Str Print BinOpMod Str NameLoad Expr Call NameLoad Str NameLoad SubscriptLoad NameLoad Index Str NameLoad SubscriptLoad NameLoad Index Str NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad NameLoad Call NameLoad Str ListLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameStore NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Str Print BinOpMod Str NameLoad Expr Call NameLoad Str NameLoad SubscriptLoad NameLoad Index Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameStore NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Str Print BinOpMod Str NameLoad Expr Call NameLoad Str NameLoad SubscriptLoad NameLoad Index Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Str Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad NameLoad NameLoad decorator_list Call NameLoad ListLoad NameLoad NameLoad Call NameLoad Str ListLoad BinOpMod Str NameLoad BinOpMod Str NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Print BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameStore NameLoad Print BinOpMod Str NameLoad Expr Call NameLoad Str NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameStore NameLoad Print BinOpMod Str NameLoad Expr Call NameLoad Str NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Index Num Print BinOpMod Str NameLoad Expr Call NameLoad Str NameLoad SubscriptLoad NameLoad Index Str NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad NameLoad Call NameLoad Str ListLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Index Num Print BinOpMod Str NameLoad Expr Call NameLoad Str NameLoad SubscriptLoad NameLoad Index Str NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad NameLoad Call NameLoad Str ListLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Index Num Print BinOpMod Str NameLoad Expr Call NameLoad Str NameLoad SubscriptLoad NameLoad Index Str NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad NameLoad Call NameLoad Str ListLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Print BinOpMod Str NameLoad Expr Call NameLoad Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Print BinOpMod Str NameLoad Expr Call NameLoad Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Print BinOpMod Str NameLoad Expr Call NameLoad Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameLoad Print BinOpMod Str NameLoad Expr Call NameLoad Str NameLoad NameLoad NameLoad decorator_list Call NameLoad NameLoad Call NameLoad Str ListLoad Str Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign NameStore NameLoad Assign NameStore NameLoad Assign NameStore SubscriptLoad NameLoad Index Num Print Str Expr Call NameLoad Str NameLoad NameLoad NameLoad decorator_list Call NameLoad ListLoad NameLoad NameLoad ListLoad BinOpMod Str NameLoad BinOpMod Str NameLoad BinOpMod Str NameLoad
N/A N/A 
GATK-based variant-calling pipeline, WGS version.

Authors: Bernie Pope, Clare Sloggett, Gayle Philip.
Thanks to Dmitri Mouradov and Maria Doyle for input on the initial 
analysis design.
Thanks to Matt Wakefield for contributions to Rubra 
(https://github.com/bjpop/rubra) during pipeline development.

Description:

This program implements a workflow pipeline for next generation
sequencing variant detection using the Broad Institute's GATK for
variant calling and using ENSEMBL for basic annotation.

It uses Rubra (https://github.com/bjpop/rubra) based on the 
Ruffus library.

It supports parallel evaluation of independent pipeline stages,
and can run stages on a cluster environment.

The pipeline is configured by an options file in a python file,
including the actual commands which are run at each stage.
 N/A sys N/A re N/A os.path N/A os collections defaultdict glob * N/A shutil ruffus * rubra.utils pipeline_options rubra.utils runStageCheck mkLogFile mkDir mkForceLink input_fastq parse_and_link make_metadata_string N/A N/A metadata N/A N/A N/A N/A -R"@RG\tID:%s\tSM:%s\tPL:%s" N/A N/A metadata N/A ID N/A metadata N/A SM N/A metadata N/A PL N/A N/A ref_files N/A pipeline_options ref_files N/A working_files N/A pipeline_options working_files N/A logDir N/A N/A pipeline_options pipeline N/A logDir N/A fastq_metadata N/A defaultdict dict N/A original_fastq_files N/A N/A fastq_dir N/A working_files N/A fastq_dirs N/A N/A original_fastq_files N/A glob N/A N/A N/A os path join fastq_dir *.fastq.gz N/A N/A N/A len original_fastq_files 0 N/A N/A No input files found. Do the filenames follow the naming convention? N/A Directories searched: N/A N/A N/A join N/A working_files N/A fastq_dirs N/A N/A N/A sys exit 1 N/A N/A mkDir N/A working_files N/A fastq_symlink_dir N/A all_fastq_files N/A N/A file original_fastq_files N/A N/A symlink N/A parse_and_link file N/A working_files N/A fastq_symlink_dir fastq_metadata N/A N/A N/A all_fastq_files append symlink N/A N/A N/A pipeline_options pipeline N/A restrict_samples N/A N/A allowed_samples N/A set N/A N/A pipeline_options pipeline N/A allowed_samples N/A fastq_files N/A file N/A file N/A sorted all_fastq_files N/A N/A N/A fastq_metadata N/A N/A N/A N/A os path basename file N/A sample allowed_samples N/A N/A fastq_files N/A sorted all_fastq_files N/A Symlinked files that will be used: N/A file fastq_files N/A N/A file N/A N/A N/A Output dir is %s N/A working_files N/A output_dir N/A N/A Log dir is %s logDir N/A N/A output_dir N/A working_files N/A output_dir N/A fastqc_dir N/A N/A N/A os path join output_dir FastQC N/A N/A mkDir fastqc_dir N/A sambam_dir N/A N/A N/A os path join output_dir alignments N/A N/A mkDir sambam_dir N/A variant_dir N/A N/A N/A os path join output_dir variant_calls N/A N/A mkDir variant_dir N/A coverage_dir N/A N/A N/A os path join output_dir coverage N/A N/A mkDir coverage_dir N/A ensembl_dir N/A N/A N/A os path join output_dir ensembl N/A N/A mkDir ensembl_dir N/A results_dir N/A N/A N/A os path join output_dir results N/A N/A mkDir results_dir fastqc N/A N/A inputs outputs N/A N/A N/A 
    Run FastQC on each fastq file.
     N/A sequence inputs N/A N/A fastqc_dest flagFile outputs N/A N/A runStageCheck fastqc flagFile fastqc_dir sequence N/A N/A transform fastq_files N/A regex (.+\/)?(.+?)\.fastq\.gz N/A N/A %s/\2_fastqc fastqc_dir N/A %s/\2.fastqc.Success fastqc_dir bwaPE N/A N/A inputs outputs N/A N/A N/A 
    Aligns two paired-end fastq files to a reference genome to produce a sam file.
     N/A N/A seq1 seq2 N/A sorted inputs N/A N/A output flag_file outputs N/A fastq_name N/A N/A N/A os path basename seq1 N/A sample N/A N/A fastq_metadata N/A fastq_name N/A sample N/A runID N/A N/A fastq_metadata N/A fastq_name N/A run_id N/A lane N/A N/A fastq_metadata N/A fastq_name N/A lane N/A readgroup_metadata N/A PL SM ID ILLUMINA sample N/A %s_%s_Lane%d N/A sample runID lane N/A metadata_str N/A make_metadata_string readgroup_metadata N/A N/A bwa-mem on %s and %s N/A N/A N/A N/A os path basename seq1 N/A N/A N/A os path basename seq2 N/A N/A runStageCheck bwaMemPE flag_file metadata_str N/A ref_files N/A bwa_reference seq1 seq2 output N/A N/A collate fastq_files N/A regex .*?([^/]+)(_1|_2)\.fastq.gz N/A N/A %s/\1.sam sambam_dir N/A %s/\1.bwaPE.Success sambam_dir samToBam N/A N/A inputs outputs N/A N/A N/A 
    Convert sam to bam and sort, using Picard.
     N/A N/A output flag_file outputs N/A N/A sam _success inputs N/A N/A converting to sorted bam: %s N/A N/A N/A os path basename sam N/A N/A runStageCheck samToSortedBam flag_file sam output N/A N/A transform bwaPE N/A suffix .sam N/A .bam .samToBam.Success mergeBams N/A N/A inputs outputs N/A N/A N/A 
    Merge the sorted bams together for each sample.
    Picard should cope correctly if there is only one input.
     N/A bams N/A bam N/A N/A bam _success inputs N/A N/A output flag_file outputs N/A baminputs N/A N/A join N/A N/A INPUT=%s bam N/A bam bams N/A N/A merging %s into %s N/A N/A N/A , join N/A N/A N/A N/A os path basename bam N/A bam bams N/A N/A N/A os path basename output N/A N/A runStageCheck mergeBams flag_file baminputs output N/A N/A collate samToBam N/A regex (.*?)([^/_]+)_([^/_]+_[^/_]+)\.bam N/A \1\2.bam \1\2.mergeBams.Success dedup N/A N/A inputs outputs N/A N/A N/A 
    Remove apparent duplicates from merged bams using Picard MarkDuplicates.
     N/A N/A input_bam _success inputs N/A N/A output_bam flag_file outputs N/A logFile N/A mkLogFile logDir input_bam .dedup.log N/A N/A de-duping %s N/A N/A N/A os path basename input_bam N/A N/A runStageCheck dedup flag_file input_bam logFile output_bam N/A N/A follows indexMergedBams N/A transform mergeBams N/A suffix .bam N/A .dedup.bam .bam.dedup.Success realignIntervals N/A N/A inputs outputs N/A N/A N/A 
    Run GATK RealignTargetCreator to find suspect intervals for realignment.
     N/A N/A bam _success inputs N/A N/A output_intervals flag_file outputs N/A logFile N/A mkLogFile logDir bam .realignIntervals.log N/A N/A calculating realignment intervals for %s N/A N/A N/A os path basename bam N/A N/A runStageCheck realignIntervals flag_file N/A ref_files N/A fasta_reference bam N/A ref_files N/A indels_realign_goldstandard N/A ref_files N/A indels_realign_1000G logFile output_intervals N/A N/A follows indexDedupedBams N/A transform dedup N/A suffix .bam N/A .realigner.intervals .bam.realignIntervals.Success remove_GATK_bai N/A N/A bamfile N/A N/A N/A 
    A bug in some versions of GATK cause it to create an x.bai file, and this gets in the way of using the properly named x.bam.bai file. If the given file exists, delete it.
     N/A bad_bai N/A N/A N/A N/A N/A os path splitext bamfile N/A 0 .bai N/A N/A N/A N/A N/A os remove bad_bai N/A N/A N/A OSError N/A e N/A N/A N/A N/A e errno 2 N/A N/A e N/A realign N/A N/A inputs outputs N/A N/A N/A 
    Run GATK IndelRealigner for local realignment, using intervals found by realignIntervals.
     N/A N/A N/A intervals _success N/A input_bam inputs N/A N/A output_bam flag_file outputs N/A logFile N/A mkLogFile logDir input_bam .realign.log N/A N/A realigning %s N/A N/A N/A os path basename input_bam N/A N/A runStageCheck realign flag_file N/A ref_files N/A fasta_reference input_bam intervals logFile output_bam N/A N/A remove_GATK_bai output_bam N/A N/A transform realignIntervals N/A regex (.*?)([^/]+)\.realigner\.intervals N/A add_inputs N/A \1\2.bam N/A \1\2.realigned.bam \1\2.bam.realign.Success baseQualRecalCount N/A N/A inputs outputs N/A N/A N/A 
    GATK CountCovariates, first step of base quality score recalibration.
     N/A N/A bam _success inputs N/A N/A output_csv flag_file outputs N/A logFile N/A mkLogFile logDir bam .baseQualRecalCount.log N/A N/A count covariates using GATK for base quality score recalibration: %s N/A N/A N/A os path basename bam N/A N/A runStageCheck baseQualRecalCount flag_file bam N/A ref_files N/A fasta_reference N/A ref_files N/A dbsnp logFile output_csv N/A N/A follows indexRealignedBams N/A transform realign N/A suffix .bam N/A .recal_data.csv .baseQualRecalCount.Success baseQualRecalTabulate N/A N/A inputs outputs N/A N/A N/A 
    GATK TableRecalibration: recalibrate base quality scores using the output of CountCovariates.
     N/A N/A N/A input_csv _success N/A input_bam inputs N/A N/A output_bam flag_file outputs N/A logFile N/A mkLogFile logDir input_bam .baseQualRecalTabulate.log N/A N/A recalibrate base quality scores using GATK on %s N/A N/A N/A os path basename input_bam N/A N/A runStageCheck baseQualRecalTabulate flag_file input_bam N/A ref_files N/A fasta_reference input_csv logFile output_bam N/A N/A remove_GATK_bai output_bam N/A N/A transform baseQualRecalCount N/A regex (.*?)([^/]+)\.recal_data\.csv N/A add_inputs N/A \1\2.bam N/A \1\2.recal.bam \1\2.baseQualRecalTabulate.Success indexRecalibratedBams N/A N/A inputs outputs N/A N/A N/A 
    Index the recalibrated bams using samtools. 
     N/A N/A bam _success inputs N/A N/A output flag_file outputs N/A N/A samtools index on %s N/A N/A N/A os path basename bam N/A N/A runStageCheck indexBam flag_file bam N/A N/A transform baseQualRecalTabulate N/A suffix .bam N/A .bam.bai .bam.indexRecalibratedBams.Success callSNPs N/A N/A inputs outputs N/A N/A N/A 
    Use GATK UnifiedGenotyper to call SNPs from recalibrated bams.
     N/A N/A bam _success inputs N/A N/A output_vcf _idx flag_file outputs N/A logFile N/A mkLogFile logDir bam .callSNPs.log N/A N/A calling SNPs from %s bam N/A N/A runStageCheck callSNPs flag_file N/A ref_files N/A fasta_reference bam N/A ref_files N/A dbsnp logFile output_vcf N/A N/A follows indexRecalibratedBams N/A transform baseQualRecalTabulate N/A regex (.*?)([^/]+)\.recal\.bam N/A N/A %s/\2.SNP.vcf variant_dir N/A %s/\2.SNP.vcf.idx variant_dir N/A %s/\2.callSNPs.Success variant_dir callIndels N/A N/A inputs outputs N/A N/A N/A 
    Use GATK UnifiedGenotyper to call indels from recalibrated bams.
     N/A N/A bam _success inputs N/A N/A output_vcf _idx flag_file outputs N/A logFile N/A mkLogFile logDir bam .callIndels.log N/A N/A calling Indels from %s bam N/A N/A runStageCheck callIndels flag_file N/A ref_files N/A fasta_reference bam N/A ref_files N/A dbsnp logFile output_vcf N/A N/A follows indexRecalibratedBams N/A transform baseQualRecalTabulate N/A regex (.*?)([^/]+)\.recal\.bam N/A N/A %s/\2.INDEL.vcf variant_dir N/A %s/\2.INDEL.vcf.idx variant_dir N/A %s/\2.callIndels.Success variant_dir filterSNPs N/A N/A inputs outputs N/A N/A N/A 
    Use GATK VariantFiltration to filter raw SNP calls.
     N/A N/A input_vcf _idx _success inputs N/A N/A output_vcf _idxout flag_file outputs N/A logFile N/A mkLogFile logDir input_vcf .filterSNPs.log N/A N/A filtering SNPs from %s input_vcf N/A N/A runStageCheck filterSNPs flag_file N/A ref_files N/A fasta_reference input_vcf logFile output_vcf N/A N/A transform callSNPs N/A suffix .SNP.vcf N/A .SNP.filtered.vcf .SNP.filtered.vcf.idx .filterSNPs.Success filterIndels N/A N/A inputs outputs N/A N/A N/A 
    Use GATK VariantFiltration to filter raw INDEL calls.
     N/A N/A input_vcf _idx _success inputs N/A N/A output_vcf _idxout flag_file outputs N/A logFile N/A mkLogFile logDir input_vcf .filterIndels.log N/A N/A filtering indels from %s input_vcf N/A N/A runStageCheck filterIndels flag_file N/A ref_files N/A fasta_reference input_vcf logFile output_vcf N/A N/A transform callIndels N/A suffix .INDEL.vcf N/A .INDEL.filtered.vcf .INDEL.filtered.vcf.idx .filterIndels.Success getEnsemblAnnotations N/A N/A inputs outputs N/A N/A N/A 
    Annotate vcf using ENSEMBL variant effect predictor.
     N/A N/A vcf _idx _success inputs N/A N/A output flag_file outputs N/A logFile N/A mkLogFile logDir vcf .EnsemblAnnotation.log N/A N/A Annotating %s with ENSEMBL variant effect predictor N/A N/A N/A os path basename vcf N/A N/A runStageCheck annotateEnsembl flag_file vcf output logFile N/A N/A transform N/A filterSNPs filterIndels N/A regex .*?([^/]+)\.vcf N/A N/A %s/\1.ensembl.vcf ensembl_dir N/A %s/\1.getEnsemblAnnotations.Success ensembl_dir indexMergedBams N/A N/A inputs outputs N/A N/A N/A 
    Index the merged bams using samtools.
     N/A N/A bam _success inputs N/A N/A output flag_file outputs N/A N/A samtools index on %s N/A N/A N/A os path basename bam N/A N/A runStageCheck indexBam flag_file bam N/A N/A transform mergeBams N/A suffix .bam N/A .bam.bai .bam.indexMergedBams.Success indexDedupedBams N/A N/A inputs outputs N/A N/A N/A 
    Index the de-duplicated bams using samtools. Note that this actually goes from the fixMate-ed bams.
     N/A N/A bam _success inputs N/A N/A output flag_file outputs N/A N/A samtools index on %s N/A N/A N/A os path basename bam N/A N/A runStageCheck indexBam flag_file bam N/A N/A transform dedup N/A suffix .bam N/A .bam.bai .bam.indexDedupedBams.Success indexRealignedBams N/A N/A inputs outputs N/A N/A N/A 
    Index the locally realigned bams using samtools.
     N/A N/A bam _success inputs N/A N/A output flag_file outputs N/A N/A samtools index on %s N/A N/A N/A os path basename bam N/A N/A runStageCheck indexBam flag_file bam N/A N/A transform realign N/A suffix .bam N/A .bam.bai .bam.indexRealignedBams.Success igvcountMergedBams N/A N/A inputs outputs N/A N/A N/A 
    Use igvtools count to create a .tdf file for the merged bam files, to improve viewing of the bam coverage in igv.
     N/A N/A bam _success inputs N/A N/A outfile flag_file outputs N/A N/A igvtools count on %s N/A N/A N/A os path basename bam N/A N/A runStageCheck igvcount flag_file bam outfile N/A N/A transform mergeBams N/A suffix .bam N/A .bam.tdf .bam.igvcountMergedBams.Success igvcountRealignedBams N/A N/A inputs outputs N/A N/A N/A 
    Use igvtools count to create a .tdf file for the merged bam files, to improve viewing of the bam coverage in igv.
     N/A N/A bam _success inputs N/A N/A outfile flag_file outputs N/A N/A igvtools count on %s N/A N/A N/A os path basename bam N/A N/A runStageCheck igvcount flag_file bam outfile N/A N/A transform realign N/A suffix .bam N/A .bam.tdf .bam.igvcountRealignedBams.Success igvcountDedupedBams N/A N/A inputs outputs N/A N/A N/A 
    Use igvtools count to create a .tdf file for the deduped bam files, to improve viewing of the bam coverage in igv. Note that this actually goes from the fixMate-ed bams.
     N/A N/A bam _success inputs N/A N/A outfile flag_file outputs N/A N/A igvtools count on %s N/A N/A N/A os path basename bam N/A N/A runStageCheck igvcount flag_file bam outfile N/A N/A transform dedup N/A suffix .bam N/A .bam.tdf .bam.igvcountDedupedBams.Success igvcountRecalibratedBams N/A N/A inputs outputs N/A N/A N/A 
    Use igvtools count to create a .tdf file for the recalibrated bam files, to improve viewing of the bam coverage in igv.
     N/A N/A bam _success inputs N/A N/A outfile flag_file outputs N/A N/A igvtools count on %s N/A N/A N/A os path basename bam N/A N/A runStageCheck igvcount flag_file bam outfile N/A N/A transform baseQualRecalTabulate N/A suffix .bam N/A .bam.tdf .bam.igvcountRecalibratedBams.Success vcfIndexSNPs N/A N/A inputs outputs N/A N/A N/A 
    Use bgzip and tabix to prepare raw SNPs vcf for vcftools handling.
     N/A N/A vcf _idx _success inputs N/A N/A zipfile tabix_index flag_file outputs N/A N/A bgzip and tabix (for vcftools) on %s vcf N/A N/A runStageCheck indexVCF flag_file vcf N/A N/A transform filterSNPs N/A suffix .vcf N/A .vcf.gz .vcf.gz.tbi .vcfindexSNPs.Success vcfIndexIndels N/A N/A inputs outputs N/A N/A N/A 
    Use bgzip and tabix to prepare raw indels vcf for vcftools handling.
     N/A N/A vcf _idx _success inputs N/A N/A zipfile tabix_index flag_file outputs N/A N/A bgzip and tabix (for vcftools) on %s vcf N/A N/A runStageCheck indexVCF flag_file vcf N/A N/A transform filterIndels N/A suffix .vcf N/A .vcf.gz .vcf.gz.tbi .vcfindexIndels.Success earlyDepthOfCoverage N/A N/A inputs outputs N/A N/A N/A 
    Use GATK DepthOfCoverage to get a first pass at coverage statistics, after merging bams.
     N/A N/A bam _success inputs N/A flag_file N/A outputs N/A -1 N/A output_example N/A outputs N/A 0 N/A output_base N/A N/A N/A N/A os path splitext output_example N/A 0 N/A N/A calculating coverage statistics using GATK DepthOfCoverage on %s bam N/A N/A runStageCheck depthOfCoverage flag_file N/A ref_files N/A fasta_reference bam output_base N/A N/A follows indexMergedBams N/A transform mergeBams N/A regex (.*?)([^/]+)\.bam N/A N/A %s/\2.early.DepthOfCoverage.sample_cumulative_coverage_counts coverage_dir N/A %s/\2.early.DepthOfCoverage.sample_cumulative_coverage_proportions coverage_dir N/A %s/\2.early.DepthOfCoverage.sample_interval_statistics coverage_dir N/A %s/\2.early.DepthOfCoverage.sample_interval_summary coverage_dir N/A %s/\2.early.DepthOfCoverage.sample_statistics coverage_dir N/A %s/\2.early.DepthOfCoverage.sample_summary coverage_dir N/A %s/\2.earlyDepthOfCoverage.Success coverage_dir dedupedDepthOfCoverage N/A N/A inputs outputs N/A N/A N/A 
    Use GATK DepthOfCoverage to get a coverage statistics as soon as duplicates are removed.
     N/A N/A bam _success inputs N/A flag_file N/A outputs N/A -1 N/A output_example N/A outputs N/A 0 N/A output_base N/A N/A N/A N/A os path splitext output_example N/A 0 N/A N/A calculating coverage statistics using GATK DepthOfCoverage on %s bam N/A N/A runStageCheck depthOfCoverage flag_file N/A ref_files N/A fasta_reference bam output_base N/A N/A follows indexDedupedBams N/A transform dedup N/A regex (.*?)([^/]+)\.dedup\.bam N/A N/A %s/\2.deduped.DepthOfCoverage.sample_cumulative_coverage_counts coverage_dir N/A %s/\2.deduped.DepthOfCoverage.sample_cumulative_coverage_proportions coverage_dir N/A %s/\2.deduped.DepthOfCoverage.sample_interval_statistics coverage_dir N/A %s/\2.deduped.DepthOfCoverage.sample_interval_summary coverage_dir N/A %s/\2.deduped.DepthOfCoverage.sample_statistics coverage_dir N/A %s/\2.deduped.DepthOfCoverage.sample_summary coverage_dir N/A %s/\2.dedupedDepthOfCoverage.Success coverage_dir finalDepthOfCoverage N/A N/A inputs outputs N/A N/A N/A 
    Use GATK DepthOfCoverage to get coverage statistics.
     N/A N/A bam _success inputs N/A flag_file N/A outputs N/A -1 N/A output_example N/A outputs N/A 0 N/A output_base N/A N/A N/A N/A os path splitext output_example N/A 0 N/A N/A calculating coverage statistics using GATK DepthOfCoverage on %s bam N/A N/A runStageCheck depthOfCoverage flag_file N/A ref_files N/A fasta_reference bam output_base N/A N/A follows indexRecalibratedBams N/A transform baseQualRecalTabulate N/A regex (.*?)([^/]+)\.recal\.bam N/A N/A %s/\2.DepthOfCoverage.sample_cumulative_coverage_counts coverage_dir N/A %s/\2.DepthOfCoverage.sample_cumulative_coverage_proportions coverage_dir N/A %s/\2.DepthOfCoverage.sample_interval_statistics coverage_dir N/A %s/\2.DepthOfCoverage.sample_interval_summary coverage_dir N/A %s/\2.DepthOfCoverage.sample_statistics coverage_dir N/A %s/\2.DepthOfCoverage.sample_summary coverage_dir N/A %s/\2.depthOfCoverage.Success coverage_dir countRunBam N/A N/A inputs outputs N/A N/A N/A 
    Run samtools flagstat on the initial per-lane, per-run bam file.
     N/A N/A bam _success inputs N/A N/A output flag_file outputs N/A N/A Running samtools flagstat on %s bam N/A N/A runStageCheck flagstat flag_file bam output N/A N/A transform samToBam N/A suffix .bam N/A .bam.flagstat .bam.countRunBam.Success countMergedBam N/A N/A inputs outputs N/A N/A N/A 
    Run samtools flagstat on the merged bam file.
     N/A N/A bam _success inputs N/A N/A output flag_file outputs N/A N/A Running samtools flagstat on %s bam N/A N/A runStageCheck flagstat flag_file bam output N/A N/A transform mergeBams N/A suffix .bam N/A .bam.flagstat .bam.countRunBam.Success countRealignedBam N/A N/A inputs outputs N/A N/A N/A 
    Run samtools flagstat on the realigned bam file.
     N/A N/A bam _success inputs N/A N/A output flag_file outputs N/A N/A Running samtools flagstat on %s bam N/A N/A runStageCheck flagstat flag_file bam output N/A N/A transform realign N/A suffix .bam N/A .bam.flagstat .bam.countRealignedBam.Success countDedupedBam N/A N/A inputs outputs N/A N/A N/A 
    Run samtools flagstat on the deduped bam file.
     N/A N/A bam _success inputs N/A N/A output flag_file outputs N/A N/A Running samtools flagstat on %s bam N/A N/A runStageCheck flagstat flag_file bam output N/A N/A transform dedup N/A suffix .bam N/A .bam.flagstat .bam.countDedupedBam.Success collateReadCounts N/A N/A inputs outputs N/A N/A N/A 
    Collate read counts from samtools flagstat output into a table.
     N/A in_dir sambam_dir N/A out_dir results_dir N/A flag_file N/A outputs N/A -1 N/A Collating read counts N/A N/A runStageCheck collateReadcounts flag_file in_dir out_dir N/A N/A merge N/A countDedupedBam countMergedBam N/A N/A %s/readcounts.txt results_dir N/A %s/readcount_fractions.txt results_dir N/A %s/collateReadcounts.Success results_dir