Bug fix: cutadapt report for paired-end read 1 and 2 were written to the same file
Added BQSR diagnostics (analyze covariates remaining after recalibration) according to GATK best practice docs
Changed rule for mergeing flowcell BAMs to sample BAMs in Makefile.halo, in order not to have unneccessary dependencies. As a result, it is no longer necessary to run "make -t samples" in HaloPlex workflow. Also changed some variable defs to use ":=" for increased speed.
Fix issued issue introduced in last commit, by reordering includes and variable assignments. Also set VariantEval options to stratify by sample (useful for HaloPlex, where there are typically many samples).
HaloPlex pipeline: changed N-masking of initial parts of reads to soft clipping. This avoids underestimation of QD (qualty by depth).
HaloPlex pipeline: added alternative recipe for variant calling, not using the merged VCF file but instead the individual BAMs. Creating the merged VCF can take very long (e.g. 16h on 1 core for a project with 196 samples sequenced on 2 flow cells; the command cannot be parallelized). This new alternative recipe provides a faster route (for the same example: 2.5h on 16 cores for variant calling from individual files, compared to 1h using the merged file).
Modified "Percent aligned reads per sample, grouped by flowcell" plot to be more informative (previous color scheme did not distinguish flow cells clearly).
Modified Picard metrics rules to work even if fastq filename does not contain sample ID. Also removed some redundant operations from these rules.
New script plotVariantEvalBySample.R for plotting GATK VariantEval results
Added rule for variant eval plot to Makefile.halo
Added variable GATK_LOG_LEVEL to control GATK verbosity
Made variant filtering criteria more stringent in Makefile.halo. Based on evaluation of results for DCM project.