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

versions.yml:file

File containing software versions

versions.yml

Tools

Github user TCLamnidis
Ask a question on Slack Open an issue on GitHub