Description

Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is available.

Input

Name (Type)
Description
Pattern

meta (map)

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

plp_prefix (string)

Prefix of pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup.

bam (file)

Input SAM/BAM/CRAM file without running popscle/dsc_pileup, must be sorted by coordinates and indexed.

*.{bam,cram,sam}

donor_genotype (file)

Input VCF/BCF file, containing the individual genotypes (GT), posterior probability (GP), or genotype likelihood (PL) to assign each barcode to a specific sample (or a pair of samples) in the VCF file.

*.{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

demuxlet_result (file)

Result of demuxlet containing the best guess of the sample identity, with detailed statistics to reach to the best guess.

*.best
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