Calculated genotype likelihoods from BAM files.
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}
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘test’ ]
fasta{:bash}
A reference genome in FASTA format
*.fasta
meta3{:bash}
error_file{:bash}
A file containing information about type specific errors.
*.error.chunkunordered
genotype_likelihood{:bash}
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
*.{glf,beagle}.gz{:bash}
File containing genotype likelihoods per sample
*.{glf,beagle}.gz
versions_angsd{:bash}
${task.process}{:bash}
:string
The name of the process
angsd{:bash}
The name of the tool
angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
ANGSD: Analysis of next generation Sequencing Data
