Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

icounts{:bash}

:file

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

*.icnts.gz

meta2{:bash}

:map

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

hapmap_file{:bash}

:file

A list of variable sites to look for heterozygosity.

Output

name:type
description
pattern

txt{:bash}

meta{:bash}

:map

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

*.txt{:bash}

:file

Contamination estimation output.

*.txt

versions_angsd{:bash}

${task.process}{:bash}

:string

The name of the process

angsd{:bash}

:string

The name of the tool

angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

angsd{:bash}

:string

The name of the tool

angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'{:bash}

:eval

The expression to obtain the version of the tool

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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