Call variants using freebayes, then sort and index
Input
name
description
pattern
meta
Groovy Map containing sample information
e.g. [ id:‘test’ ]
input1
BAM/CRAM/SAM file;
*.{bam,cram,sam}
index1
Index BAI/CRAI/CSI file
*.{bai,crai,csi}
input2
BAM/CRAM/SAM file; used to run variant calling with pair (normal vs tumor)
*.{bam,cram,sam}
index2
Index BAI/CRAI/CSI file
*.{bai,crai,csi}
bed
Optional - Limit analysis to targets listed in this BED-format FILE.
*.bed
meta2
Groovy Map containing reference information
e.g. [ id:‘test’ ]
fasta
reference fasta file
.{fa,fa.gz,fasta,fasta.gz}
fai
reference fasta file index
*.{fa,fasta}.fai
samples
Optional - Limit analysis to samples listed (one per line) in the FILE.
*.txt
populations
Optional - Each line of FILE should list a sample and a population which it is part of.
*.txt
cnv
A copy number map BED file, which has either a sample-level ploidy:
sample_name copy_number
or a region-specific format:
seq_name start end sample_name copy_number
*.bed
Output
name
description
pattern
meta
Groovy Map containing sample information
e.g. [ id:‘test’ ]
versions
File containing software versions
versions.yml
vcf
Sorted VCF file
*.{vcf.gz}
csi
Default VCF file index file
*.csi
tbi
Alternative VCF file index file (activated with -t parameter)
