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ReblockGVCF is now out of beta (#7419)
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Also add some docs details
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ldgauthier authored Aug 18, 2021
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*
* <p>
* 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.</p>
*
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* <h3>Usage example</h3>
* <pre>
* 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
* </pre>
*
* Invocation as for use with GnarlyGenotyper in the "Biggest Practices"
* Invocation as for smallest GVCFs to use with GnarlyGenotyper
* <pre>
* gatk ReblockGVCF \
* -R reference.fasta \
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*
* <h3>Caveats</h3>
* <p>Only single-sample GVCF files produced by HaplotypeCaller can be used as input for this tool.</p>
* <p>Annotations and header lines that are uninformative for single-sample will be dropped:
* MLEAC, MLEAF, DS, ExcessHet, HaplotypeScore, InbreedingCoeff, AS_InbreedingCoeff
* <p>Note that when uncalled alleles are dropped, the original GQ may increase. Use --keep-all-alts if GQ accuracy is a concern.</p>
*
*/
@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 {

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