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

demuxlet_result

meta:map

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

*.best:file

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

*.best

versions

versions.yml:file

File containing software versions

versions.yml

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
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