/cb_sniffer

mutation(barcode) caller for 10x single cell data

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

cb_sniffer

Mutation barcode caller, calls mutant and ref barcodes from 10x single cell data
Bams aligned using 10x cellranger pipeline

Usage

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

Variant file

chrm	start	stop	ref	var	gene_name	trv_type
19	4xxx	4xxx	G	A	gene_name	silent/misense/frame_shift

barcodes

AACCTGAGAATGTTG-1
AAACCTGAGCTACCGC-1
AAACCTGAGCTGCCCA-1
AAACCTGAGGTCGGAT-1
AAACCTGAGTACGATA-1
AAACCTGAGTGCAAGC-1
AAACCTGAGTGCCATT-1
AAACCTGAGTGGAGTC-1
AAACCTGCAAAGTGCG-1
AAACCTGCATAAGACA-1

Output files

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

Dependencies

python3
pysam

Docker image

  • sridnona/python3:180925.v1
LSF_DOCKER_PRESERVE_ENVIRONMENT=false bsub -Is -q research-hpc -a "docker(sridnona/python3:180925.v1)" /bin/bash