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Reference model import code is borked #1568

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fnothaft opened this issue Jun 15, 2017 · 0 comments
Closed

Reference model import code is borked #1568

fnothaft opened this issue Jun 15, 2017 · 0 comments
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@fnothaft fnothaft commented Jun 15, 2017

These three genotypes are all split from a single gVCF line with 3 variants and a symbolic model:

{"variant": {"contigName": "chr22", "start": 18030095, "end": 18030099, "names": [], "referenceAllele": "TAAA", "alternateAllele": "T", "filtersApplied": false, "filtersPassed": null, "filtersFailed": [], "\
annotation": {"ancestralAllele": null, "alleleCount": null, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "referenceRe\
verseReadDepth": null, "alleleFrequency": null, "cigar": null, "dbSnp": null, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attrib\
utes": {"MQRankSum": "-0.686", "MQ": "69.72", "MLEAC": "0", "BaseQRankSum": "-0.133", "ClippingRankSum": "-1.438", "MLEAF": "0.00", "ReadPosRankSum": "-0.013", "DP": "114", "MQ0": "0"}}}, "contigName": "chr\
22", "start": 18030095, "end": 18030099, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue"\
: null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "\
NA12878i", "sampleDescription": null, "processingDescription": null, "alleles": ["OTHER_ALT", "OTHER_ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 13, "alternateReadDepth": 3, "readDepth": 50, \
"minReadDepth": null, "genotypeQuality": 86, "genotypeLikelihoods": [0.0, 0.0, 0.0], "nonReferenceLikelihoods": [0.0, 0.0, 0.0], "strandBiasComponents": [], "splitFromMultiAllelic": true, "phased": false, "\
phaseSetId": null, "phaseQuality": null}
{"variant": {"contigName": "chr22", "start": 18030095, "end": 18030099, "names": [], "referenceAllele": "TAAA", "alternateAllele": "TA", "filtersApplied": false, "filtersPassed": null, "filtersFailed": [], \
"annotation": {"ancestralAllele": null, "alleleCount": null, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "referenceR\
everseReadDepth": null, "alleleFrequency": null, "cigar": null, "dbSnp": null, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attri\
butes": {"MQRankSum": "-0.686", "MQ": "69.72", "MLEAC": "1", "BaseQRankSum": "-0.133", "ClippingRankSum": "-1.438", "MLEAF": "0.500", "ReadPosRankSum": "-0.013", "DP": "114", "MQ0": "0"}}}, "contigName": "c\
hr22", "start": 18030095, "end": 18030099, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValu\
e": null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId":\
 "NA12878i", "sampleDescription": null, "processingDescription": null, "alleles": ["ALT", "OTHER_ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 13, "alternateReadDepth": 17, "readDepth": 50, "mi\
nReadDepth": null, "genotypeQuality": 86, "genotypeLikelihoods": [0.0, -2.5118865E-9, 0.0], "nonReferenceLikelihoods": [0.0, "-Infinity", 0.0], "strandBiasComponents": [], "splitFromMultiAllelic": true, "ph\
ased": false, "phaseSetId": null, "phaseQuality": null}
{"variant": {"contigName": "chr22", "start": 18030095, "end": 18030099, "names": [], "referenceAllele": "TAAA", "alternateAllele": "TAA", "filtersApplied": false, "filtersPassed": null, "filtersFailed": [],\
 "annotation": {"ancestralAllele": null, "alleleCount": null, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "reference\
ReverseReadDepth": null, "alleleFrequency": null, "cigar": null, "dbSnp": null, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attr\
ibutes": {"MQRankSum": "-0.686", "MQ": "69.72", "MLEAC": "1", "BaseQRankSum": "-0.133", "ClippingRankSum": "-1.438", "MLEAF": "0.500", "ReadPosRankSum": "-0.013", "DP": "114", "MQ0": "0"}}}, "contigName": "\
chr22", "start": 18030095, "end": 18030099, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPVal\
ue": null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId"\
: "NA12878i", "sampleDescription": null, "processingDescription": null, "alleles": ["OTHER_ALT", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 13, "alternateReadDepth": 17, "readDepth": 50, "m\
inReadDepth": null, "genotypeQuality": 86, "genotypeLikelihoods": [0.0, -1.9984014E-14, 0.0], "nonReferenceLikelihoods": [0.0, 0.0, 0.0], "strandBiasComponents": [], "splitFromMultiAllelic": true, "phased":\
 false, "phaseSetId": null, "phaseQuality": null}

Alas, they have different non-reference likelihoods, which just ain't right. These are from adam-core/src/test/resources/gvcf_dir/gvcf_multiallelic.g.vcf.

@fnothaft fnothaft added the bug label Jun 15, 2017
@fnothaft fnothaft added this to the 0.23.0 milestone Jun 15, 2017
@fnothaft fnothaft self-assigned this Jun 15, 2017
fnothaft added a commit to fnothaft/adam that referenced this issue Jun 19, 2017
Resolves bigdatagenomics#1568. Fixes a bug where the wrong non-reference allele index was set
for multiallelic sites with >1 known alternate allele and a non-reference model.
fnothaft added a commit to fnothaft/adam that referenced this issue Jun 19, 2017
Resolves bigdatagenomics#1568. Fixes a bug where the wrong non-reference allele index was set
for multiallelic sites with >1 known alternate allele and a non-reference model.
fnothaft added a commit to fnothaft/adam that referenced this issue Jun 19, 2017
Resolves bigdatagenomics#1568. Fixes a bug where the wrong non-reference allele index was set
for multiallelic sites with >1 known alternate allele and a non-reference model.
fnothaft added a commit to fnothaft/adam that referenced this issue Jun 22, 2017
Resolves bigdatagenomics#1568. Fixes a bug where the wrong non-reference allele index was set
for multiallelic sites with >1 known alternate allele and a non-reference model.
@heuermh heuermh closed this in 34feb3d Jun 22, 2017
@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018
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