Description

Software to pileup reads and corresponding base quality for each overlapping SNPs and each barcode.

Input

Name (Type)
Description
Pattern

meta (map)

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

bam (file)

Input SAM/BAM/CRAM file produced by the standard 10x sequencing platform, or any other barcoded single cell RNA-seq.

*.{bam,cram,sam}

vcf (file)

Input VCF/BCF file files containing (AC) and (AN) from referenced population (e.g. 1000g).

*.{vcf,bcf}

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

cel (file)

Contains the relation between numerated barcode ID and barcode and the number of SNP and number of UMI for each barcoded droplet.

*.cel.gz

plp (file)

Contains the overlapping SNP and the corresponding read and base quality for each barcode ID.

*.plp.gz

var (file)

Contains the position, reference allele and allele frequency for each SNP.

*.var.gz

umi (file)

Contains the position covered by each umi.

*.umi.gz
maintainers
Github user mari-ga
Github user maxozo
Github user wxicu
Github user Zethson
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

popscle
Apache-2.0

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

github.com/statgen/popscle 10.1038/nbt.4042