brentp
commented
7 years ago as you've found, platypus is not supported. We support RO/AO (as in freebayes) or AD (as in GATK and the VCF spec) for REF, ALT depths. I'm not sure why GQ is not supported, but it does look like your header is missing the sample name (after "FORMAT")
ehitchcock
Hello,
I am not able to filter variants based on depth or genotype quality. I used Platypus to call my variants. I saw in already posted issues that this problem is due to Gemini only supporting this information from GATK and FreeBayes.
I was wondering if you could please tell me how this information is supposed to be reported in my vcf file?
Thank you very much!
Below is the header of my vcf and a SNP from my vcf:
fileformat=VCFv4.0
FILTER=
fileDate=2017-05-11
source=Platypus_Version_0.8.1
platypusOptions={'assemblyRegionSize': 1500, 'trimReadFlank': 0, 'assembleBadReads': 1, 'bamFiles': ['CAU7EANXX_1_CGATGT_A1335.bam'], 'minVarDist': 9, 'trimSoftClipped': 1, 'minReads': 2, 'qualBinSize': 1, 'refFile': 'GRCh37-lite.fa', 'maxHaplotypes': 50, 'filterVarsByCoverage': 1, 'maxSize': 1500, 'originalMaxHaplotypes': 50, 'skipDifficultWindows': 0, 'parseNCBI': 0, 'skipRegionsFile': None, 'noCycles': 0, 'trimAdapter': 1, 'minPosterior': 5, 'assembleAll': 1, 'trimOverlapping': 1, 'filterDuplicates': 1, 'abThreshold': 0.001, 'minFlank': 10, 'bufferSize': 100000, 'fileCaching': 0, 'useEMLikelihoods': 0, 'coverageSamplingLevel': 30, 'calculateFlankScore': 0, 'logFileName': 'CAU7EANXX_1_CGATGT_A1335.platvarlog.txt', 'nCPU': 1, 'filterReadsWithUnmappedMates': 1, 'qdThreshold': 10, 'maxVariants': 8, 'scThreshold': 0.95, 'filterReadsWithDistantMates': 1, 'maxReads': 5000000, 'badReadsWindow': 11, 'genIndels': 1, 'largeWindows': 0, 'minMapQual': 20, 'maxVarDist': 15, 'maxGOF': 30, 'rlen': 150, 'minGoodQualBases': 20, 'refCallBlockSize': 1000, 'countOnlyExactIndelMatches': 0, 'longHaps': 0, 'HLATyping': 0, 'filterReadPairsWithSmallInserts': 1, 'minBaseQual': 20, 'getVariantsFromBAMs': 1, 'genSNPs': 1, 'assemble': 0, 'assemblerKmerSize': 15, 'minVarFreq': 0.05, 'alignScoreFile': '', 'verbosity': 2, 'sourceFile': None, 'compressReads': 0, 'rmsmqThreshold': 40, 'filteredReadsFrac': 0.7, 'outputRefCalls': 0, 'badReadsThreshold': 15, 'hapScoreThreshold': 4, 'regions': None, 'sbThreshold': 0.001, 'output': 'CAU7EANXX_1_CGATGT_A1335_Platypus.vcf', 'assembleBrokenPairs': 0, 'mergeClusteredVariants': 1, 'maxGenotypes': 1275, 'nInd': 1}
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SnpEffVersion="4.3i (build 2016-12-15 22:33), by Pablo Cingolani"
SnpEffCmd="SnpEff -i vcf -o vcf GRCh37.75 /Users/ehitchcock/A1335/CAU7EANXX_1_CGATGT_A1335_Platypus_normalized.vcf "
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CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
10 105128134 . T G 926.0 PASS BRF=0.5;FR=0.5;HP=3;HapScore=2;MGOF=5;MMLQ=34;MQ=58.73;NF=10;NR=24;PP=926;QD=28.258;SC=AGTGGCGGGCTCCGGAGCCCC;SbPval=0.53;Source=Platypus;TC=80;TCF=23;TCR=57;TR=34;WE=105128142;WS=105128124;ANN=G|missense_variant|MODERATE|TAF5|ENSG00000148835|transcript|ENST00000369839|protein_coding|1/11|c.388T>G|p.Ser130Ala|411/3268|388/2403|130/800||,G|missense_variant|MODERATE|TAF5|ENSG00000148835|transcript|ENST00000351396|protein_coding|1/10|c.388T>G|p.Ser130Ala|411/3099|388/2238|130/745|GT:GL:GOF:GQ:NR:NV 1/0:-96.65,0,-105.05:5:99:80:34
(cc: @Phillip-a-richmond)