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

]

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.

calling_method (value)

The desired calling method for pileupcaller. One of ‘randomHaploid’, ‘randomDiploid’, or ‘majorityCall’.

output_format (value)

The desired output format. One of ‘PLINK’, ‘EIGENSTRAT’, or ‘FREQSUM’.

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

eigenstrat (file)

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

*.{geno,snp,ind}.txt

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

*.{bed,bim,fam}

freqsum (file)

The output freqsum-formatted file.

*.freqsum.gz
author
Github user TCLamnidis
get in touch
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Tools

sequencetools
MIT

Tools for population genetics on sequencing data

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