modules/cellsnp_modea

Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use the mode A of cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs for droplet based single cell data.

genotypingsingle cellSNPdroplet based single cells

https://github.com/nf-core/modules/[...]/modules/nf-core/cellsnp/modea

Description

Input

name:type

description

pattern

`meta:map`

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

`bam:file`

A single BAM/SAM/CRAM file, e.g., from CellRanger.

*.{bam,cram,sam}

`bai:file`

The index of the BAM/CRAM file.

*.{bai,crai}

`region_vcf:file`

A optional vcf file listing all candidate SNPs for genotyping.

*.{vcf, vcf.gz}

`barcode:file`

A plain file listing all effective cell barcodes.

*.tsv

Output

name:type

description

pattern

`base`

`meta:map`

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

`*.base.vcf.gz:file`

A VCF file listing genotyped SNPs and aggregated AD & DP infomation (without GT).

*.base.vcf.gz

`cell`

`meta:map`

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

`*.cells.vcf.gz:file`

A VCF file listing genotyped SNPs and aggregated AD & DP infomation & genotype (GT) information for each cell or sample.

*.cells.vcf.gz

`sample`

`meta:map`

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

`*.samples.tsv:file`

A TSV file listing cell barcodes or sample IDs.

*.tsv

`allele_depth`

`meta:map`

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

`*.tag.AD.mtx:file`

A file in “Matrix Market exchange formats”, containing the allele depths of the alternative (ALT) alleles.

*.tag.AD.mtx

`depth_coverage`

`meta:map`

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

`*.tag.DP.mtx:file`

A file in “Matrix Market exchange formats”, containing the sum of allele depths of the reference and alternative alleles (REF + ALT).

*.tag.DP.mtx

`depth_other`

`meta:map`

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

`*.tag.OTH.mtx:file`

A file in “Matrix Market exchange formats”, containing the sum of allele depths of all the alleles other than REF and ALT.

*.tag.OTH.mtx

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

cellsnp
Apache-2.0

Efficient genotyping bi-allelic SNPs on single cells

github.com/single-cell-genetics/cellsnp-lite cellsnp-lite.readthedocs.io https://github.com/single-cell-genetics/cellsnp-lite 10.1093/bioinformatics/btab358

modules/cellsnp_modea

Description

Input

`meta:map`

`bam:file`

`bai:file`

`region_vcf:file`

`barcode:file`

Output

`base`

`meta:map`

`*.base.vcf.gz:file`

`cell`

`meta:map`

`*.cells.vcf.gz:file`

`sample`

`meta:map`

`*.samples.tsv:file`

`allele_depth`

`meta:map`

`*.tag.AD.mtx:file`

`depth_coverage`

`meta:map`

`*.tag.DP.mtx:file`

`depth_other`

`meta:map`

`*.tag.OTH.mtx:file`

`versions`

`versions.yml:file`

Tools

cellsnp
Apache-2.0

maintainer

get in touch

modules/cellsnp_modea

Description

Input

meta:map

bam:file

bai:file

region_vcf:file

barcode:file

Output

base

meta:map

*.base.vcf.gz:file

cell

meta:map

*.cells.vcf.gz:file

sample

meta:map

*.samples.tsv:file

allele_depth

meta:map

*.tag.AD.mtx:file

depth_coverage

meta:map

*.tag.DP.mtx:file

depth_other

meta:map

*.tag.OTH.mtx:file

versions

versions.yml:file

Tools

cellsnp Apache-2.0

maintainer

get in touch

`meta:map`

`bam:file`

`bai:file`

`region_vcf:file`

`barcode:file`

`base`

`meta:map`

`*.base.vcf.gz:file`

`cell`

`meta:map`

`*.cells.vcf.gz:file`

`sample`

`meta:map`

`*.samples.tsv:file`

`allele_depth`

`meta:map`

`*.tag.AD.mtx:file`

`depth_coverage`

`meta:map`

`*.tag.DP.mtx:file`

`depth_other`

`meta:map`

`*.tag.OTH.mtx:file`

`versions`

`versions.yml:file`

cellsnp
Apache-2.0