Tools for population-scale genotyping using pangenome graphs.
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
bam{:bash}
:file
BAM/CRAM file
*.{bam,cram}
bai{:bash}
:file
BAM index file. This is automatically found base on BAM input file name
*.{bai}
meta2{:bash}
:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
ref{:bash}
:file
Reference fasta file
*.{fa, fasta, fas}
meta3{:bash}
:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
ref_fai{:bash}
:file
Reference index file. This is automatically found based on reference input file name.
*.{.fai}
region_file{:bash}
:file
File with a list of chromosome/locations in reference genome to genotype. One region per line in the format :-. This or --region (in ext.args) must be specified.
*
Output
name:type
description
pattern
vcf{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
results/*/*.vcf.gz{:bash}
:file
VCF file with genotyped variants
*.{vcf.gz}
tbi{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
results/*/*.vcf.gz.tbi{:bash}
:file
VCF index file
*.{vcf.gz.tbi}
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
graphtyper
MIT
A graph-based variant caller capable of genotyping population-scale short read data sets while incorporating previously discovered variants.
