mutract 1.1

Extracting single cell variants from bam file

Mutract

Mutract is a tool for extracting single cell variants from bam file. If vcf file is not provided, it will perform variant calling at single cell level.

Requirements

• python > 3.6
• GATK
• samtools

Installation

pip install mutract

GATK and samtools can be installed via conda.

Usage

mutract \
--bam bam_file \
--barcodes cell_barcodes_file \
--fasta reference_fasta_file \
--vcf vcf_file \
--sample sample_name \
--outdir output_directory \
--thread 8 \
--gene_file gene_file \

• Required Arguments

bam Input CeleScope BAM file. If gene_file is specified, the BAM must have the 'GN' tag.

barcodes Cell barcodes file, one barcode per line.

fasta Reference genome fasta, must be indexed.

sample Sample name.

• Optional Arguments

vcf VCF file. If vcf file is not provided, mutract will perform variant calling at single cell level and use these variants as input vcf.

outdir Output directory, default='./'.

thread The number of threads to use, default=1.

gene_file Gene list file, one gene symbol per line. Only variants of these genes are reported.

Output

{sample}_VID.tsv A unique numeric ID is assigned for each variant.

{sample}_CID.tsv A unique numeric ID is assigned for each cell.

{sample}_variant_count.tsv Reference and variant supporting reads/UMIs count.

{sample}_support.mtx Support matrix, only high quality bases are considered.
0 : no reads/UMIs cover the position.
1 : all reads/UMIs at the position support the ref allele.
2 : all reads/UMIs at the position support the alt allele.
3 : one or more reads/UMIs support both the alt and the ref allele.