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 not available.

Input

Name (Type)
Description
Pattern

meta (map)

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

plp (directory)

Directory contains pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup.

n_sample (integer)

Number of samples multiplexed together.

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

result (file)

Output file contains the best guess of the sample identity, with detailed statistics to reach to the best guess.

*.clust1.samples.gz

vcf (file)

Output vcf file for each sample inferred and clustered from freemuxlet.

*.clust1.vcf.gz

lmix (file)

Output file contains basic statistics for each barcode.

*.lmix

singlet_result (file)

Optional output file contains the best sample identity assuming all droplets are singlets when writing auxiliary output files is turned on.

*.clust0.samples.gz

singlet_vcf (file)

Optional output vcf file for each sample inferred and clustered from freemuxlet assuming all droplets are singlets when writing auxiliary output files is turned on.

*.clust0.vcf.gz
maintainer
Github user wxicu
get in touch
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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