# graphtyper 2.7.5


{{< admonition success "Installed" true >}}
This software should be available with no extra configuration.
{{< /admonition >}}

## 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

```sh
./graphtyper genotype <REFERENCE.fa> --sams=<BAMLIST_OR_CRAMLIST> --region=<chrA:begin-end> --threads=<T>
```

and use the `genotype_sv` subcommand for genotyping structural variants

```sh
./graphtyper genotype_sv <REFERENCE.fa> <input.vcf.gz> --sams=<BAMLIST_OR_CRAMLIST> --region=<chrA:begin-end> --threads=<T>
```

See the 
[graphtyper user guide](https://github.com/DecodeGenetics/graphtyper/wiki/User-guide)
for more details.

-------------------------------------------------------------------------------

## Location

```console
$ which graphtyper
/local/cluster/bin/graphtyper
```

## help message

```console
$ 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
```

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>