Description

Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval.

Input

name:type
description
pattern

meta:map

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

input:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

input_index:file

BAM/CRAM/SAM index file

*.{bai,crai,sai}

intervals:file

A file containing the specified intervals

*.{bed,intervals}

meta2:map

Groovy Map containing reference information e.g. [ id:‘test’ ]

fasta:file

Optional - Reference FASTA

*.{fasta,fa}

meta3:map

Groovy Map containing reference information e.g. [ id:‘test’ ]

fai:file

Optional - Index of the reference FASTA file

*.fai

meta4:map

Groovy Map containing reference information e.g. [ id:‘test’ ]

dict:file

Optional - Sequence dictionary of the reference FASTA file

*.dict

Output

name:type
description
pattern

hdf5

meta:map

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

*.hdf5:file

The read counts in hdf5 format

*.hdf5

tsv

meta:map

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

*.tsv:file

The read counts in TSV format

*.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

gatk4
Apache-2.0

Genome Analysis Toolkit (GATK4). 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/articles/360037593911-CombineGVCFs https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590
included in
createpanelrefs raredisease
maintainer
Github user nvnieuwk
get in touch
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