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

]

meta2 (map)

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

meta3 (map)

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

meta4 (map)

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

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}

fasta (file)

Optional - Reference FASTA

*.{fasta,fa}

fai (file)

Optional - Index of the reference FASTA file

*.fai

dict (file)

Optional - Sequence dictionary of the reference FASTA file

*.dict

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

hdf5 (file)

The read counts in hdf5 format

*.hdf5

tsv (file)

The read counts in TSV format

*.tsv
included in
createpanelrefs raredisease
maintainer
Github user nvnieuwk
get in touch
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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