Description

Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use the mode A of cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs for droplet based single cell data.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

bam (file)

A single BAM/SAM/CRAM file, e.g., from CellRanger.

*.{bam,cram,sam}

bai (file)

The index of the BAM/CRAM file.

*.{bai,crai}

region_vcf (file)

A optional vcf file listing all candidate SNPs for genotyping.

*.{vcf, vcf.gz}

barcode (file)

A plain file listing all effective cell barcodes.

*.tsv

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

versions (file)

File containing software versions

versions.yml

base (file)

A VCF file listing genotyped SNPs and aggregated AD & DP infomation (without GT).

*.base.vcf.gz

cell (file)

A VCF file listing genotyped SNPs and aggregated AD & DP infomation & genotype (GT) information for each cell or sample.

*.cells.vcf.gz

sample (file)

A TSV file listing cell barcodes or sample IDs.

*.tsv

allele_depth (file)

A file in “Matrix Market exchange formats”, containing the allele depths of the alternative (ALT) alleles.

*.tag.AD.mtx

depth_coverage (file)

A file in “Matrix Market exchange formats”, containing the sum of allele depths of the reference and alternative alleles (REF + ALT).

*.tag.DP.mtx

depth_other (file)

A file in “Matrix Market exchange formats”, containing the sum of allele depths of all the alleles other than REF and ALT.

*.tag.OTH.mtx
maintainer
Github user wxicu
get in touch
Ask a question on Slack Open an issue on GitHub

Tools