Description

Calculates base frequency statistics across reference positions from BAM.

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

A list of BAM or CRAM files

*.{bam,cram}

bai{:bash}

:file

List of BAM/CRAM index files

*.{bai,csi}

minqfile{:bash}

:file

File with individual quality score thresholds

*

Output

name:type
description
pattern

depth_sample{:bash}

meta{:bash}

:map

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

*.depthSample{:bash}

:file

Distribution of sequencing depths

*.depthSample

depth_global{:bash}

meta{:bash}

:map

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

*.depthGlobal{:bash}

:file

Distribution of sequencing depths

*.depthGlobal

qs{:bash}

meta{:bash}

:map

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

*.qs{:bash}

:file

Distribution of scores

*.qs

pos{:bash}

meta{:bash}

:map

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

*.pos.gz{:bash}

:file

Various types of depth statistics (depending on value for -dumpCounts)

*.pos.gz

counts{:bash}

meta{:bash}

:map

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

*.counts.gz{:bash}

:file

Various types of statistics (related to pos.gz)

*.counts.gz

icounts{:bash}

meta{:bash}

:map

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

*.icnts.gz{:bash}

:file

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

*.icnts.gz

versions{:bash}

versions.yml{:bash}

: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 jfy133
get in touch
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