Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

: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{:bash}

:file

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

*.{vcf,bcf}

Output

name:type
description
pattern

cel{:bash}

meta{:bash}

:map

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

*.cel.gz{:bash}

: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{:bash}

meta{:bash}

:map

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

*.plp.gz{:bash}

:file

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

*.plp.gz

var{:bash}

meta{:bash}

:map

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

*.var.gz{:bash}

:file

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

*.var.gz

umi{:bash}

meta{:bash}

:map

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

*.umi.gz{:bash}

:file

Contains the position covered by each umi.

*.umi.gz

versions{:bash}

versions.yml{:bash}

: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 auxiliary 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