Mercurial > repos > jjohnson > gatk2
changeset 12:b40671bc73d5 draft
Add help to HaplotypeCaller
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Thu, 08 Nov 2012 10:55:32 -0600 (2012-11-08) |
parents | 5faf7ace8aee |
children | da03516b528c |
files | haplotype_caller.xml |
diffstat | 1 files changed, 27 insertions(+), 0 deletions(-) [+] |
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--- 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**