Description

Calculates the allele-specific read counts for allele-specific expression analysis of RNAseq data

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

bam:file

BAM file

*.{bam}

bai:file

index file for BAM file

*.{bai}

vcf:file

VCF file

*.{vcf.gz}

tbi:file

index file for VCF file

*.{vcf.gz.tbi}

meta2:map

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

fasta:file

fasta file

*.{fasta,fa}

meta3:map

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

fai:file

fasta index file

*.{fai}

meta4:map

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

dict:file

dictionary file

*.{dict}

intervals:file

interval file

Output

name:type
description
pattern

csv

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

versions

versions.yml:file

File containing software versions

versions.yml

Tools

gatk4
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s 10.1158/1538-7445.AM2017-3590
Github user Lucpen
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