detect snv and small indel using pysam pileup method
python3 pileup2vaf.py -bam $bam -bed $bed -fa $fa -od $PWD -n "rawbam"
usage: Detect snv and small indel using pysam pileup method
[-h] [-bam BAM] [-bed BED] [-d DEPTH] [-n NAME] [-mq MAPQ] [-bq BASEQ]
[-fa FASTA] [-od OUTDIR]
optional arguments:
-h, --help show this help message and exit
-bam BAM bam file
-bed BED bed file
-d DEPTH max depth
-n NAME samplel name
-mq MAPQ map quality
-bq BASEQ base quality
-fa FASTA fasta file
-od OUTDIR output dir
-bam: input bam file
-bed: BED file
-fa : reference fasta file
-d : max depth limit, same as samtools mpileup. [default: 8000]
-n : sample name
-mq : mapping quailty cutoff. [default: 0]
-bq : base quality. [default: 0]
-od : output dir
less test/cmd.sh
python3 ../pileup2vaf.py -bam $line -bed $bed -fa $fa -od $PWD -n $name
The outfile is <sample_name>.variants.xls
Chr Pos Ref Alt AltNum Depth AltAlleleFrequency
chr12 52380364 T ref-homo 0 24 0.0
chr12 52380365 T C 1 24 0.042
chr12 52380366 A ref-homo 0 24 0.0
chr12 52380623 TGATGA T 90 582 0.155
chrX 48649699 C CTACT 30 155 0.194
- Python3
- Pysam