Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix. - pysam/bcftools/mpileup.c at 6b4
call.h cols.c cols.h config.mk.in configure.ac consensus.c convert.c csq.c doc bcftools.1 bcftools.html bcftools.txt filter.c gvcf.c hex.h main.c mcall.c misc demo-flt.pl guess-ploidy.py plot-roh.py plot-vcfstats vcfutils.pl mpileup.c plugins ...
RC17-1_L003.sorted.rmp.rg.recal.bam RC17-2_L004.sorted.rmp.rg.recal.bam RC17-3_L004.sorted.rmp.rg.recal.bam 数据准备好后，执行命令：samtools mpileup -P ILLUMINA -f RAP_cDAN.fasta -EgD \ LC17-1_L002.sorted.rmp.rg.recal.bam LC17-2_L006.sorted.rmp.rg.recal.bam \ ...
The indel boundaries are based on REF // (POS+1,POS+rlen-1). This is not entirely correct: mpileup likes to // output REF=CAGAGAGAGA, ALT=CAGAGAGAGAGA where REF=C,ALT=CGA could be // used. This filter is therefore more strict and may remove some valid // SNPs. ...
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix. - pysam/bcftools/vcfcall.c at 6b4
mpileup_bench plugins GTisec.c GTisec.mk GTsubset.c GTsubset.mk ad-bias.c ad-bias.mk add-variantkey.c af-dist.c af-dist.mk allele-length.c check-ploidy.c check-sparsity.c color-chrs.c color-chrs.mk contrast.c counts.c dosage.c fill-AN-AC.c fill-from-fasta.c fill-from-...
filter.c filter.h gff.c gff.h gvcf.c gvcf.h hclust.c hclust.h hex.h install-sh khash_str2str.h kheap.h kmin.c kmin.h main.c mcall.c mpileup.c mw.h peakfit.c peakfit.h ploidy.c ploidy.h polysomy.c prob1.c prob1.h rbuf.h read_consensus.c read_consensus.h regidx.c re...
filter.c filter.h gvcf.c gvcf.h hclust.c hclust.h hex.h install-sh khash_str2str.h kheap.h kmin.c kmin.h main.c mcall.c mpileup.c mw.h peakfit.c peakfit.h ploidy.c ploidy.h polysomy.c prob1.c prob1.h rbuf.h regidx.c regidx.h reheader.c smpl_ilist.c smpl_ilist.h ...