Description

Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls.

Input

name:type
description
pattern

meta:map

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

pileup:file

File containing the pileups summary table of a tumor sample to be used to calculate contamination.

*.pileups.table

matched:file

File containing the pileups summary table of a normal sample that matches with the tumor sample specified in pileup argument. This is an optional input.

*.pileups.table

Output

name:type
description
pattern

contamination

meta:file

File containing the contamination table.

*.contamination.table

*.contamination.table:file

File containing the contamination table.

*.contamination.table

segmentation

meta:file

output table containing segmentation of tumor minor allele fractions (optional)

*.segmentation.table

*.segmentation.table:file

output table containing segmentation of tumor minor allele fractions (optional)

*.segmentation.table

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
included in
rnadnavar sarek
maintainers
Github user GCJMackenzie
Github user maxulysse
get in touch
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