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