modules/angsd_docounts

Calculates base frequency statistics across reference positions from BAM.

angsdpopulation geneticsallele countsdoCounts

https://github.com/nf-core/modules/[...]/modules/nf-core/angsd/docounts

Description

Calculates base frequency statistics across reference positions from BAM.

Input

name:type

description

pattern

`meta:map`

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

]

`bam:file`

A list of BAM or CRAM files

*.{bam,cram}

`bai:file`

List of BAM/CRAM index files

*.{bai,csi}

`minqfile:file`

File with individual quality score thresholds

*

Output

name:type

description

pattern

`depth_sample`

`meta:map`

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

]

`*.depthSample:file`

Distribution of sequencing depths

*.depthSample

`depth_global`

`meta:map`

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

]

`*.depthGlobal:file`

Distribution of sequencing depths

*.depthGlobal

`qs`

`meta:map`

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

]

`*.qs:file`

Distribution of scores

*.qs

`pos`

`meta:map`

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

]

`*.pos.gz:file`

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

*.pos.gz

`counts`

`meta:map`

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

]

`*.counts.gz:file`

Various types of statistics (related to pos.gz)

*.counts.gz

`icounts`

`meta:map`

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

]

`*.icnts.gz:file`

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

*.icnts.gz

`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

modules/angsd_docounts

Description

Input

`meta:map`

`bam:file`

`bai:file`

`minqfile:file`

Output

`depth_sample`

`meta:map`

`*.depthSample:file`

`depth_global`

`meta:map`

`*.depthGlobal:file`

`qs`

`meta:map`

`*.qs:file`

`pos`

`meta:map`

`*.pos.gz:file`

`counts`

`meta:map`

`*.counts.gz:file`

`icounts`

`meta:map`

`*.icnts.gz:file`

`versions`

`versions.yml:file`

Tools

angsd
GPL v3, MIT

maintainer

get in touch

modules/angsd_docounts

Description

Input

meta:map

bam:file

bai:file

minqfile:file

Output

depth_sample

meta:map

*.depthSample:file

depth_global

meta:map

*.depthGlobal:file

qs

meta:map

*.qs:file

pos

meta:map

*.pos.gz:file

counts

meta:map

*.counts.gz:file

icounts

meta:map

*.icnts.gz:file

versions

versions.yml:file

Tools

angsd GPL v3, MIT

maintainer

get in touch

`meta:map`

`bam:file`

`bai:file`

`minqfile:file`

`depth_sample`

`meta:map`

`*.depthSample:file`

`depth_global`

`meta:map`

`*.depthGlobal:file`

`qs`

`meta:map`

`*.qs:file`

`pos`

`meta:map`

`*.pos.gz:file`

`counts`

`meta:map`

`*.counts.gz:file`

`icounts`

`meta:map`

`*.icnts.gz:file`

`versions`

`versions.yml:file`

angsd
GPL v3, MIT