Commit b0850a6f authored by Peter van 't Hof's avatar Peter van 't Hof

Added docs

parent f815eb1a
......@@ -118,6 +118,11 @@ At this moment the following variant callers can be used
| shiva | correct_readgroups | Boolean | false | Attempt to correct read groups | Only used when input is a bam file |
| shiva | amplicon_bed | Path | | Path to target bed file | all |
| shiva | regions_of_interest | Array of paths | | Array of paths to region of interest (e.g. gene panels) bed files | all |
| shivavariantcalling | gender_aware_calling | Boolean | false | Enables gander aware variantcalling | haplotypecaller_gvcf |
| shivavariantcalling | hap̦loid_regions | Bed file | | Haploid regions for all genders | haplotypecaller_gvcf |
| shivavariantcalling | hap̦loid_regions_male | Bed file | | Haploid regions for males | haplotypecaller_gvcf |
| shivavariantcalling | hap̦loid_regions_female | Bed file | | Haploid regions for females | haplotypecaller_gvcf |
| shiva | amplicon_bed | Path | | Path to target bed file | all |
| vcffilter | min_sample_depth | Integer | 8 | Filter variants with at least x coverage | raw |
| vcffilter | min_alternate_depth | Integer | 2 | Filter variants with at least x depth on the alternate allele | raw |
| vcffilter | min_samples_pass | Integer | 1 | Minimum amount of samples which pass custom filter (requires additional flags) | raw |
......@@ -130,6 +135,14 @@ For all the options, please see the corresponding documentation for the mapping
## Advanced usage
### Gender aware variantcalling
In Shiva and ShivaVariantcalling while using haplotypecaller_gvcf it is possible to do gender aware variantcalling. In this mode it required to supply bed files to define haploid regions (see config values).
- For males is `hap̦loid_regions` and `hap̦loid_regions_male` used.
- For females is `hap̦loid_regions` and `hap̦loid_regions_female` used.
The pipeline will use a union of those files. At least 1 file is required while using this mode.
### Reporting modes
Shiva furthermore supports three modes. The default and recommended option is `multisample_variantcalling`.
......
......@@ -22,6 +22,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.extensions.gatk.CombineGVCFs
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
......@@ -75,7 +76,7 @@ class HaplotypeCallerGvcf(val parent: Configurable) extends Variantcaller {
override def init(): Unit = {
super.init()
if (genderAwareCalling && haploidRegions.isEmpty && haploidRegionsMale.isEmpty && haploidRegionsFemale.isEmpty)
logger.warn("Gender aware variantcalling is enabled but no haploid bed files are given")
Logging.addError("Gender aware variantcalling is enabled but no haploid bed files are given")
}
def biopetScript() {
......
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