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