Mutation barcode caller, calls mutant and ref barcodes from 10x single cell data
Bams aligned using 10x cellranger pipeline
python3 cb_sniffer.py -h
usage: cb_sniffer.py [-h] [-f FILTER] [-mq MAPQ] [-bq BASEQ]
bam_file variant_file barcodes upn
Parse CB barcodes from Single cell rna seq data
positional arguments:
bam_file BAM file
variant_file variants file with header
barcodes list of good barcodes file
upn upn/sample name: will be used as prefix for out_file
optional arguments:
-h, --help show this help message and exit
-f FILTER, --filter FILTER
number of reads required per barcode default: 0
-mq MAPQ, --mapq MAPQ
Skip read with mapq smaller than default : 0
-bq BASEQ, --baseq BASEQ
Skip bases with base quality less than default : 1
chrm start stop ref var gene_name trv_type
19 4xxx 4xxx G A gene_name silent/misense/frame_shift
AACCTGAGAATGTTG-1
AAACCTGAGCTACCGC-1
AAACCTGAGCTGCCCA-1
AAACCTGAGGTCGGAT-1
AAACCTGAGTACGATA-1
AAACCTGAGTGCAAGC-1
AAACCTGAGTGCCATT-1
AAACCTGAGTGGAGTC-1
AAACCTGCAAAGTGCG-1
AAACCTGCATAAGACA-1
1. variant list with barcodes supporting a variant :_AllCounts.tsv
2. read counts for Chromium cellular barcode sequence(CB_tag) : _counts_CB.tsv
3. read counts for Chromium molecular barcode(UB_tag): _counts_UB.tsv
python3
pysam
LSF_DOCKER_PRESERVE_ENVIRONMENT=false bsub -Is -q research-hpc -a "docker(sridnona/python3:180925.v1)" /bin/bash