Commit 97d831f3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding some more information

parent b0e3e032
......@@ -83,6 +83,9 @@ unifiedgenotyper:
At this moment the following variant callers can be used
##### Germline
When doing variantcalling mostly germline is used. This will detect variants based on the assumption that there is a fixed number of alleles. Mostly the default used is a ploidy of 2. When this assumption does not hold for your data somatic variantcalling can be a better solution.
| ConfigName | Tool | Description |
| ---------- | ---- | ----------- |
| haplotypecaller_gvcf | <a href="https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php">haplotypecaller</a> | Running HaplotypeCaller in gvcf mode |
......@@ -97,6 +100,9 @@ At this moment the following variant callers can be used
| varscan_cns_singlesample | <a href="http://varscan.sourceforge.net/">varscan</a> | |
##### Somatic
In contrast to germline variantcalling does somatic variantcalling does not have a direct assumption about the number of alleles. Some can also take a control into account, like MuTect2. Having a control is useful when analysing tumor samples.
| ConfigName | Tool | Description |
| ---------- | ---- | ----------- |
| mutect2 | <a href="https://software.broadinstitute.org/gatk/gatkdocs/3.7-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php">MuTect2</a> | Running mutect2, requires tumor normal pairs |
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