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