modules/sequencetools_pileupcaller

PileupCaller is a tool to create genotype calls from bam files using read-sampling methods

genotypingmpileuprandom drawpseudohaploidpseudodiploidfreqsumplinkbedeigenstrat

https://github.com/nf-core/modules/[...]/modules/nf-core/sequencetools/pileupcaller

Description

PileupCaller is a tool to create genotype calls from bam files using read-sampling methods

Input

name:type

description

pattern

`meta`
`:map`

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

`mpileup`
`:file`

samtools mpileup output.

`snpfile`
`:file`

Eigenstrat format .snp file of the sites in the mpileup file to call genotypes on. Only alleles matching the Ref and Alt alleles of the provided snp file will be called.

`sample_names_fn`
`:file`

File containing the sample names

Output

name:type

description

pattern

`eigenstrat`

`meta`
`:map`

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

`*.geno`
`:file`

A tuple containing the output Eigenstrat-formatted geno, snp and ind files.

*.{geno,snp,ind}.txt

`*.snp`
`:file`

A tuple containing the output Eigenstrat-formatted geno, snp and ind files.

*.{geno,snp,ind}.txt

`*.ind`
`:file`

A tuple containing the output Eigenstrat-formatted geno, snp and ind files.

*.{geno,snp,ind}.txt

`plink`

`meta`
`:map`

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

`*.bed`
`:file`

A tuple containing the output Plink-formatted bed, bim and fam files.

*.{bed,bim,fam}

`*.bim`
`:file`

A tuple containing the output Plink-formatted bed, bim and fam files.

*.{bed,bim,fam}

`*.fam`
`:file`

A tuple containing the output Plink-formatted bed, bim and fam files.

*.{bed,bim,fam}

`freqsum`

`meta`
`:map`

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

`*.freqsum.gz`
`:file`

The output freqsum-formatted file.

*.freqsum.gz

`versions_pileupcaller`

`${task.process}`
`:string`

The name of the process

`sequencetools`
`:string`

The name of the tool

`pileupCaller --version 2>&1`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`sequencetools`
`:string`

The name of the tool

`pileupCaller --version 2>&1`
`:eval`

The expression to obtain the version of the tool

Tools

sequencetools
MIT

Tools for population genetics on sequencing data

github.com/stschiff/sequenceTools github.com/stschiff/sequenceTools#readme https://github.com/stschiff/sequenceTools

modules/sequencetools_pileupcaller

Description

Input

`meta`
`:map`

`mpileup`
`:file`

`snpfile`
`:file`

`sample_names_fn`
`:file`

Output

`eigenstrat`

`meta`
`:map`

`*.geno`
`:file`

`*.snp`
`:file`

`*.ind`
`:file`

`plink`

`meta`
`:map`

`*.bed`
`:file`

`*.bim`
`:file`

`*.fam`
`:file`

`freqsum`

`meta`
`:map`

`*.freqsum.gz`
`:file`

`versions_pileupcaller`

`${task.process}`
`:string`

`sequencetools`
`:string`

`pileupCaller --version 2>&1`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`sequencetools`
`:string`

`pileupCaller --version 2>&1`
`:eval`

Tools

sequencetools
MIT

maintainer

get in touch

modules/sequencetools_pileupcaller

Description

Input

meta :map

mpileup :file

snpfile :file

sample_names_fn :file

Output

eigenstrat

meta :map

*.geno :file

*.snp :file

*.ind :file

plink

meta :map

*.bed :file

*.bim :file

*.fam :file

freqsum

meta :map

*.freqsum.gz :file

versions_pileupcaller

${task.process} :string

sequencetools :string

pileupCaller --version 2>&1 :eval

Topics

versions

${task.process} :string

sequencetools :string

pileupCaller --version 2>&1 :eval

Tools

sequencetoolsMIT

maintainer

get in touch

`meta`
`:map`

`mpileup`
`:file`

`snpfile`
`:file`

`sample_names_fn`
`:file`

`eigenstrat`

`meta`
`:map`

`*.geno`
`:file`

`*.snp`
`:file`

`*.ind`
`:file`

`plink`

`meta`
`:map`

`*.bed`
`:file`

`*.bim`
`:file`

`*.fam`
`:file`

`freqsum`

`meta`
`:map`

`*.freqsum.gz`
`:file`

`versions_pileupcaller`

`${task.process}`
`:string`

`sequencetools`
`:string`

`pileupCaller --version 2>&1`
`:eval`

`versions`

`${task.process}`
`:string`

`sequencetools`
`:string`

`pileupCaller --version 2>&1`
`:eval`

sequencetools
MIT