The Java port of the VarDict variant caller
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bams
:file
One or two BAM files. Supply two BAM files to run Vardict in paired mode.
*.bam
bais
Index/indices of the BAM file(s)
*.bai
bed
BED with the regions of interest
*.bed
meta2
Groovy Map containing fasta information e.g. [ id:‘test’, single_end:false ]
fasta
FASTA of the reference genome
*.{fa,fasta}
meta3
fasta_fai
The index of the FASTA of the reference genome
*.fai
vcf
*.vcf.gz
VCF file output
versions_vardictjava
${task.process}
:string
The name of the process
vardict-java
The name of the tool
realpath \$( command -v vardict-java ) | sed 's/.*java-//;s/-.*//'
:eval
The expression to obtain the version of the tool
versions_var2vcfvalid
var2vcf_valid.pl
var2vcf_valid.pl -h | sed '2!d;s/.* //'
versions_htslib
htslib
tabix -h 2>&1 | sed -n '2s/Version: *//p'
versions
Java port of the VarDict variant discovery program
