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 (file)

File containing the contamination table.

*.contamination.table

segmentation (file)

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

*.segmentation.table

versions (file)

File containing software versions

versions.yml
included in
rnadnavar sarek
maintainers
Github user GCJMackenzie
Github user maxulysse
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