# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1352393732 21600
# Node ID b40671bc73d502bb3119041c1735a79a13b01366
# Parent  5faf7ace8aeed4aca2c2ad859c976fdd794a3c51
Add help to HaplotypeCaller

diff -r 5faf7ace8aee -r b40671bc73d5 haplotype_caller.xml
--- a/haplotype_caller.xml	Thu Nov 08 10:38:18 2012 -0600
+++ b/haplotype_caller.xml	Thu Nov 08 10:55:32 2012 -0600
@@ -625,6 +625,33 @@
  max_quality_score              The integer value at which to cap the quality scores, default=50
  doNotWriteOriginalQuals        If true, we will not write the original quality (OQ) tag for each read
 
+*HaplotypeCaller specific arguments*::
+ activeRegionIn              Use this interval list file as the active regions to process
+ activeRegionOut             Output the active region to this interval list file
+ alleles                     The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES
+ annotation                  One or more specific annotations to apply to variant calls
+ comp                        comparison VCF file
+ contamination               Fraction of contamination in sequencing data (for all samples) to aggressively remove
+ dbsnp                       dbSNP file
+ debug                       If specified, print out very verbose debug information about each triggering active region
+ downsampleRegion            coverage, per-sample, to downsample each active region to
+ excludeAnnotation           One or more specific annotations to exclude
+ genotyping_mode             Specifies how to determine the alternate alleles to use for genotyping
+ graphOutput                 File to which debug assembly graph information should be written
+ group                       One or more classes/groups of annotations to apply to variant calls
+ heterozygosity              Heterozygosity value used to compute prior likelihoods for any locus
+ minPruning                  The minimum allowed pruning factor in assembly graph. Paths with less than or equal supporting kmers are pruned from the graph
+ output_mode                 Specifies which type of calls we should output
+ pair_hmm_implementation     The PairHMM implementation to use for genotype likelihood calculations
+ stand_call_conf             The minimum phred-scaled confidence threshold at which variants should be called
+ stand_emit_conf             The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)
+ useAllelesTrigger           If specified, use additional trigger on variants found in an external alleles file
+ fullHaplotype               If specified, output the full haplotype sequence instead of converting to individual variants w.r.t. the reference
+ gcpHMM                      Flat gap continuation penalty for use in the Pair HMM
+ genotypeFullActiveRegion    If specified, alternate alleles are considered to be the full active region for the purposes of genotyping
+ max_alternate_alleles       Maximum number of alternate alleles to genotype
+ p_nonref_model              Non-reference probability calculation model to employ
+
 ------
 
 **Citation**