Description

A tool to estimate nuclear contamination in males based on heterozygosity in the female chromosome.

Input

name:type
description
pattern

meta:map

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

icounts:file

Internal format for dumping binary single chrs. Useful for ANGSD contamination

*.icnts.gz

meta2:map

Groovy Map containing information related to the hapmap_file. e.g. [ id:‘test’ ]

hapmap_file:file

A list of variable sites to look for heterozygosity.

Output

name:type
description
pattern

txt

meta:map

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

*.txt:file

Contamination estimation output.

*.txt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

angsd
GPL v3 MIT

ANGSD: Analysis of next generation Sequencing Data

http://www.popgen.dk/angsd https://github.com/ANGSD/angsd 10.1186/s12859-014-0356-4
maintainer
Github user jbv2
get in touch
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