Installed
This software should be available with no extra configuration.
graphtyper-2.7.5
graphtyper is a graph-based variant caller capable of genotyping
population-scale short read data sets. It represents a reference genome and
known variants of a genomic region using an acyclic graph structure (a
“pangenome reference”), which high-throughput sequence reads are re-aligned to
for the purpose of discovering and genotyping SNPs, small indels, and
structural variants.
Usage
The recommended way of genotyping small variants (SNP+indels) is using the
genotype subcommand
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./graphtyper genotype <REFERENCE.fa> --sams=<BAMLIST_OR_CRAMLIST> --region=<chrA:begin-end> --threads=<T>
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and use the genotype_sv subcommand for genotyping structural variants
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./graphtyper genotype_sv <REFERENCE.fa> <input.vcf.gz> --sams=<BAMLIST_OR_CRAMLIST> --region=<chrA:begin-end> --threads=<T>
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See the
graphtyper user guide
for more details.
Location
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$ which graphtyper
/local/cluster/bin/graphtyper
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help message
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$ graphtyper --help
NAME
GraphTyper
USAGE
graphtyper <subcommand> [OPTIONS]
<subcommand>
Subcommand to execute. List of available subcommands are shown in the
following section.
SUBCOMMANDS
bamshrink Run bamShrink.
call Call variants of a graph.
check Check a GraphTyper graph (useful for debugging).
construct Construct a graph.
genotype Run the SNP/indel genotyping pipeline.
genotype_camou (WIP) Run the camou SNP/indel genotyping pipeline.
genotype_hla (WIP) Run the HLA genotyping pipeline.
genotype_lr (WIP) Run the camou LR genotyping pipeline.
genotype_sv Run the structural variant (SV) genotyping pipeline.
index (deprecated) Index a graph.
vcf_break_down Break down/decompose a VCF file.
vcf_concatenate Concatenate VCF files.
vcf_merge Merge VCF files.
OPTIONS
--log=value or -lvalue
Set path to log file.
--verbose or -v
Set to output verbose logging.
--vverbose
Set to output very verbose logging.
--help or -h
Show this help.
VERSION
2.7.5
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software ref: https://github.com/DecodeGenetics/graphtyper
research ref: https://doi.org/10.1038/ng.3964
research ref: https://doi.org/10.1038/s41467-019-13341-9