Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

input_index (file)

index file for input file

*.{bai,crai}

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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

csv (file)

output file

*.{csv}
maintainer
Github user Lucpen
get in touch
Ask a question on Slack Open an issue on GitHub

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