@@ -56,6 +56,8 @@ class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with Sca
@Argument(fullName="maxGGAARExtension",shortName="maxGGAARExtension",doc="the maximum extent into the full active region extension that we're willing to go in genotyping our events for GGA mode",required=false,exclusiveOf="",validation="")
/** Include at least this many bases around an event for calling indels */
@Argument(fullName="paddingAroundIndels",shortName="paddingAroundIndels",doc="Include at least this many bases around an event for calling indels",required=false,exclusiveOf="",validation="")
/** Parses a vcf-file and counts sv-s by type and size. Sv-s are divided to different size classes, the parameter histogramBinBoundaries gives the boundaries between these classes. */
| 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 |
...
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@@ -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, `hap̦loid_regions` and `hap̦loid_regions_male` is used.
- For females, `hap̦loid_regions` and `hap̦loid_regions_female` is 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`.