Commit d9308ceb authored by Peter van 't Hof's avatar Peter van 't Hof

Changes from review

parent 5ef2f11d
......@@ -82,7 +82,6 @@ At this moment the following variant callers can be used
| 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 |
| haplotypecaller_allele | <a href="https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php">haplotypecaller</a> | 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> | Only genotype a given list of alleles with UnifiedGenotyper |
......@@ -220,6 +219,7 @@ shiva:
sv_callers:
- breakdancer
- delly
- clever
pysvtools:
flanking: 100
```
......
# Introduction
# Invocation
# Example
Note that one should first create the appropriate [configs](../general/config.md).
# Testcase A
# Testcase B
# Examine results
## Result files
## Best practice
# References
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