diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java index 9b730f86bfe..77a2aff4a50 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java @@ -49,7 +49,8 @@ * *

* ReblockGVCF compresses a GVCF by merging hom-ref blocks that were produced using the '-ERC GVCF' or '-ERC BP_RESOLUTION' mode of the - * HaplotypeCaller according to new GQ band parameters. A joint callset produced with GVCFs reprocessed by ReblockGVCF will have + * HaplotypeCaller according to new GQ band parameters. Uncalled alleles and associated data will also be dropped unless --keep-all-alts is specified. + * A joint callset produced with GVCFs reprocessed by ReblockGVCF will have * lower precision for hom-ref genotype qualities at variant sites, but the input data footprint can be greatly reduced * if the default GQ band parameters are used.

* @@ -66,12 +67,13 @@ *

Usage example

*
  * gatk ReblockGVCF \
+ *   -GQB 20 -GQB 30 -GQB 40 --floor-blocks \
  *   -R reference.fasta \
  *   -V sample1.g.vcf \
- *   -O sample1.reblocked.g.vcf
+ *   -O sample1.rb.g.vcf
  * 
* - * Invocation as for use with GnarlyGenotyper in the "Biggest Practices" + * Invocation as for smallest GVCFs to use with GnarlyGenotyper *
  *  gatk ReblockGVCF \
  *    -R reference.fasta \
@@ -84,14 +86,14 @@
  *
  * 

Caveats

*

Only single-sample GVCF files produced by HaplotypeCaller can be used as input for this tool.

+ *

Annotations and header lines that are uninformative for single-sample will be dropped: + * MLEAC, MLEAF, DS, ExcessHet, HaplotypeScore, InbreedingCoeff, AS_InbreedingCoeff *

Note that when uncalled alleles are dropped, the original GQ may increase. Use --keep-all-alts if GQ accuracy is a concern.

* */ -@BetaFeature @CommandLineProgramProperties(summary = "Compress a single-sample GVCF from HaplotypeCaller by merging homRef blocks using new GQ band parameters", oneLineSummary = "Condenses homRef blocks in a single-sample GVCF", - programGroup = OtherProgramGroup.class, - omitFromCommandLine = true) + programGroup = OtherProgramGroup.class) @DocumentedFeature public final class ReblockGVCF extends MultiVariantWalker {