Commit f634582b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding more information about variantcallers

parent 08e4b344
...@@ -78,16 +78,19 @@ A dry run can be performed by simply removing the `-run` flag from the command l ...@@ -78,16 +78,19 @@ A dry run can be performed by simply removing the `-run` flag from the command l
## Variant caller ## Variant caller
At this moment the following variant callers can be used At this moment the following variant callers can be used
`TODO: explain them briefly` * <a href="https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php">haplotypecaller</a>
* Running default HaplotypeCaller
* haplotypecaller * <a href="https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php">haplotypecaller_gvcf</a>
* haplotypecaller_gvcf * Running HaplotypeCaller in gvcf mode
* haplotypecaller_allele * <a href="https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php">haplotypecaller_allele</a>
* unifiedgenotyper * Only genotype a given list of alleles with HaplotypeCaller
* unifiedgenotyper_allele * <a href="https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_genotyper_UnifiedGenotyper.php">unifiedgenotyper</a>
* bcftools * Running default UnifiedGenotyper
* freebayes * <a href="https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_genotyper_UnifiedGenotyper.php">unifiedgenotyper_allele</a>
* raw * Only genotype a given list of alleles with UnifiedGenotyper
* <a href="https://samtools.github.io/bcftools/bcftools.html">bcftools</a>
* <a href="https://github.com/ekg/freebayes">freebayes</a>
* [raw](../tools/MpileupToVcf)
## Config options ## Config options
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