Adding some more information

docs/pipelines/multisample/shiva.md

@@ -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 |