Description

Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD.

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

BAM/CRAM file to be summarised.

*.{bam,cram}

index{:bash}

:file

Index file for the input BAM/CRAM file.

*.{bam.bai,cram.crai}

intervals{:bash}

:file

File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically.

*.interval_list

meta2{:bash}

:map

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

fasta{:bash}

:file

The reference fasta file

*.fasta

meta3{:bash}

:map

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

fai{:bash}

:file

Index of reference fasta file

*.fasta.fai

meta4{:bash}

:map

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

dict{:bash}

:file

GATK sequence dictionary

*.dict

variants{:bash}

:file

Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.

*.vcf.gz

variants_tbi{:bash}

:file

Index file for the germline resource.

*.vcf.gz.tbi

Output

name:type
description
pattern

table{:bash}

meta{:bash}

:map

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

*.pileups.table{:bash}

:file

Table containing read counts for each site.

*.pileups.table

versions{:bash}

versions.yml{:bash}

: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
included in
rnadnavarsarek
maintainer
Github user GCJMackenzie
get in touch
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