Package: readcomb
readcomb- fast detection of recombinant reads in BAMsreadcombis a collection of command line and Python tools for fast detection
of recombination events in pooled high-throughput sequencing data.readcombsearches for changes in parental haplotype phase across individual reads and classifies
recombination events based on various properties of the observed recombinant haplotypes.readcombwas designed for use with the model algaChlamydomonas reinhardtiiand
currently only supports haploids. Although the means of specifically detecting gene
conversion are more specific toC. reinhardtii, everything else inreadcombis
generalizable to the detection of recombination events in any haploid species.InstallationpipinstallreadcombDependenciescyvcf2- Fast retrieval and filtering of VCF files and VCF objects written in Cpysam- Interface for SAM and BAM files and provides SAM and BAM objectspandas- Support for data tablestqdm- Provides updating progress bars for command line programssamtools- Used for preprocessing of VCF and BAM filesUsage:bamprepCommand line preprocessing script for BAM files.bamprepwill prepare an
index file, filter out unusuable reads, and output a BAMsorted by read name.readcombrequires BAMs sorted by read name for fast parsing and filtering.readcomb-bamprep--bam[bam_filepath]--out[outdir]Optional parameters:--samtools- Path to samtools binary--threads [int]- Number of threads samtools should use (default 1)--index_csi- Create CSI index instead of BAI--no_progress- Disable index creation - this will speed upbamprepbut
will mean no progress bars when filteringvcfprepCommand line preprocessing script for VCF filesreadcomb-vcfprep--vcf[vcf_filepath]--out[output_filepath]Optional arguments--snps_only- Keep only SNPs--indels_only- Keep only indels--no_hets- Remove heterozygote calls--min_GQ [int]- Minimum genotype quality at both sites (default 30)filterCommand line multiprocessing script for identification of bam sequences with phase changesreadcomb-filter--bam[bam_filepath]--vcf[vcf_filepath]Optional arguments:-p, --processes [processes], Number of processes available for filter (default 4)-m, --mode [phase_change|no_match], Filtering mode (defaultphase_change)-l, --log [log_filepath], Filename for log metric output-o, --out [output_filepath], File to write filtered output to (defaultrecomb_diagnosis)classificationPython module for detailed classification of sequences containing phase changes>>>importreadcomb.classificationasrc>>>fromcyvcf2importVCF>>>bam_filepath='data/example_sequences.bam'>>>vcf_filepath='data/example_variants.vcf.gz'>>>pairs=rc.pairs_creation(bam_filepath,vcf_filepath)# generate list of Pair objects>>>cyvcf_object=VCF(vcf_filepath)# cyvcf2 file object>>>print(pairs[0])Recordname:chromosome_1-199370Read1:chromosome_1:499417-499667Read2:chromosome_1:499766-500016VCF:data/example_variants.vcf.gz>>>pairs[0].classify(cyvcf_object)# run classification algorithm>>>print(pairs[0])Recordname:chromosome_1-199370Read1:chromosome_1:499417-499667Read2:chromosome_1:499766-500016VCF:data/example_variants.vcf.gzUnmatchedVariant(s):FalseCondensed:[['CC2936',499417,499626],['CC2935',499626,499736],['CC2936',499736,500016]]Call:gene_conversionCondensedMasked:[['CC2936',499487,499626],['CC2935',499626,499736],['CC2936',499736,499946]]CallMasked:gene_conversionLicenseGNU General Public License v3 (GPLv3+)DevelopmentCurrently in alphaSource codeDevelopment repo