issue in the vcf format using Mutect2

Question

[arshiya.g02]

filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives.

source=Mutect2

tumor_sample=unit2

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unit2

chr1 58764709 . A AATTCATTATTATTTGTCGTTAAATACAATAGAAAATACTATACCTGTATATGCAATTCGTCAATAGATAAATTATTAAATATGCTTACAACAATCTTAATATCCTTTAACGCACTACAATAGTGCT . . DP=1 ECNT=1 MBQ=0 20 MFRL=0 22 MMQ=60 54 MPOS=1 POPAF=7.30 TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0 1:0.667:1:0 0:0 1:0 0 0 1 chr1 105918966 . A AAATATTATTTCTGCGCTGCCTCTTTATAATCGCAATTTGAACATATTACTTGTGTTGTCTTGCCTTTTTTATTTTCAACAAGATATTGGTTACATTTTGGACAATCTCTTCCAATCGGCTTAT . . DP=1 ECNT=1 MBQ=0 20 MFRL=0 21 MMQ=60 40 MPOS=3 POPAF=7.30 TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0 1:0.667:1:0 0:0 1:0 0 0 1 chr1 195693453 . A ATCAAGATTCGCAATGGAAAGATGAGACGTTATTTAAATTACAACGTCAGTTTGCATACACGAAAGAAGAGATTCATAAGTATATTCAGGAACTTGTAGAAGGTAAGAAGGATCCTATCGGTGC . . DP=1 ECNT=1 MBQ=0 20 MFRL=0 21 MMQ=60 42 MPOS=5 POPAF=7.30 TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0 1:0.667:1:0 0:0 1:0 0 0 1 chr10 34569099 . A ACCATCTTTAAAACCTGCTTAAGTGCTTCGTCAGTATCAGTAATCACAGCATCACTTTCTTTTCTACTAAC . . DP=1 ECNT=3 MBQ=0 20 MFRL=0 22 MMQ=60 49 MPOS=10 POPAF=7.30 TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 1:0.667:1:0 0:0 1:0|1:34569099_A_ACCATCTTTAAAACCTGCTTAAGTGCTTCGTCAGTATCAGTAATCACAGCATCACTTTCTTTTCTACTAAC:34569099:0 0 0 1 chr10 34569101 . A AGCTGCCCATCATCTTCGTATCGTCTATC . . DP=1 ECNT=3 MBQ=0 35 MFRL=0 22 MMQ=60 49 MPOS=8 POPAF=7.30 TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 1:0.667:1:0 0:0 1:0|1:34569099_A_ACCATCTTTAAAACCTGCTTAAGTGCTTCGTCAGTATCAGTAATCACAGCATCACTTTCTTTTCTACTAAC:34569099:0 0 0 1 chr10 34569105 . A AAACACTTCAGAAGCTGTAATT . . DP=1 ECNT=3 MBQ=0 40 MFRL=0 22 MMQ=60 49 MPOS=4 POPAF=7.30 TLOD=4.13 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 1:0.667:1:0 0:0 1:0|1:34569099_A_ACCATCTTTAAAACCTGCTTAAGTGCTTCGTCAGTATCAGTAATCACAGCATCACTTTCTTTTCTACTAAC:34569099:0 0 0 1 chr11 42310850 . G GCATA . . DP=2 ECNT=6 MBQ=0 20 MFRL=0 21 MMQ=60 39 MPOS=16 POPAF=7.30 TLOD=8.52 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 2:0.750:2:0 1:0 1:0|1:42310850_G_GCATA:42310850:0 0 0 2 chr11 42310854 . T TGC . . DP=2 ECNT=6 MBQ=0 20 MFRL=0 21 MMQ=60 39 MPOS=12 POPAF=7.30 TLOD=8.52 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 2:0.750:2:0 1:0 1:0|1:42310850_G_GCATA:42310850:0 0 0 2 chr11 42310856 . CA C . . DP=2 ECNT=6 MBQ=0 20 MFRL=0 21 MMQ=60 39 MPOS=10 POPAF=7.30 TLOD=8.52 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 2:0.750:2:0 1:0 1:0|1:42310850_G_GCATA:42310850:0 0 0 2 chr11 42310861 . T TAATGCTTGCATAGGAATATCATAAATATCTATTTCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCA . . DP=2 ECNT=6 MBQ=0 20 MFRL=0 21 MMQ=60 39 MPOS=5 POPAF=7.30 TLOD=8.52 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 2:0.750:2:0 1:0 1:0|1:42310850_G_GCATA:42310850:0 0 0 2 chr11 42310864 . C CATAATA . . DP=2 ECNT=6 MBQ=0 38 MFRL=0 21 MMQ=60 39 MPOS=2 POPAF=7.30 TLOD=8.52 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 2:0.750:2:0 1:0 1:0|1:42310850_G_GCATA:42310850:0 0 0 2 chr11 42310866 . C CTACCT . . DP=2 ECNT=6 MBQ=0 35 MFRL=0 21 MMQ=60 39 MPOS=0 POPAF=7.30 TLOD=8.52 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 2:0.750:2:0 1:0 1:0|1:42310850_G_GCATA:42310850:0 0 0 2 chr11 79116108 . G GATATAATAGTTGATTGAAGTATA . . DP=1 ECNT=3 MBQ=0 20 MFRL=0 21 MMQ=60 40 MPOS=9 POPAF=7.30 TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 1:0.667:1:0 1:0 0:0|1:79116108_G_GATATAATAGTTGATTGAAGTATA:79116108:0 0 0 1 chr11 79116110 . C CGAACAGGAGTCCATCATGATTGTATATATATTAATTAATATTGCTATCGTCATACTTATA . . DP=1 ECNT=3 MBQ=0 20 MFRL=0 21 MMQ=60 40 MPOS=7 POPAF=7.30 TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 1:0.667:1:0 1:0 0:0|1:79116108_G_GATATAATAGTTGATTGAAGTATA:79116108:0 0 0 1 chr11 79116114 . G GGATTCAATTTATATAGGCATCAAATGCAACATTTATCATTA . . DP=1 ECNT=3 MBQ=0 38 MFRL=0 21 MMQ=60 40 MPOS=3 POPAF=7.30 TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 1:0.667:1:0 1:0 0:0|1:79116108_G_GATATAATAGTTGATTGAAGTATA:79116108:0 0 0 1 chr11 94431426 . A AGAAG . . DP=1 ECNT=3 MBQ=0 20 MFRL=0 21 MMQ=60 46 MPOS=10 POPAF=7.30 TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 1:0.667:1:0 1:0 0:0|1:94431426_A_AGAAG:94431426:0 0 0 1 chr11 94431430 . A ATATTAATTTTTTACAT . . DP=1 ECNT=3 MBQ=0 20 MFRL=0 21 MMQ=60 46 MPOS=6 POPAF=7.30 TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 1:0.667:1:0 1:0 0:0|1:94431426_A_AGAAG:94431426:0 0 0 1 chr11 94431432 . A AAATACGAGTTGACAGAATTATTTTTGGGGATCCAGCAGTAGTAATGTATGTGAAGGCGCAAGAGAATCCAATACCACTTCATTGGAATGCAGAGACGTTAGT . . DP=1 ECNT=3 MBQ=0 20 MFRL=0 21 MMQ=60 46 MPOS=4 POPAF=7.30 TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 1:0.667:1:0 1:0 0:0|1:94431426_A_AGAAG:94431426:0 0 0 1 chr11 105851212 . A AAAAGGACGATGTGAATG . . DP=1 ECNT=3 MBQ=0 20 MFRL=0 22 MMQ=60 41 MPOS=8 POPAF=7.30 TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 1:0.667:1:0 1:0 0:0|1:105851212_A_AAAAGGACGATGTGAATG:105851212:0 0 0 1 chr11 105851216 . T TGTGTTCGGGATTTGCACAAAGATATGTTTATATTGCAAAAATAATATGAATTTAGATGCATAAAAAAAGAAC . . DP=1 ECNT=3 MBQ=0 20 MFRL=0 22 MMQ=60 41 MPOS=4 POPAF=7.30 TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0 1:0.667:1:0 1:0 0:0|1:105851212_A_AAAAGGACGATGTGAATG:105851212:0 0 0 1

[steve]

What exactly is the question here? What program are you trying to run? You will also need to format your post better.

[bjwiley23]

Anbody know why most POPAF=7.3?

Answer 1

[2nelly]

If you are talking about the warning then this is just a warning not an error.

The produced vcf file normally contains many false positive variants. Run FilterMutectCalls using the output of MuTect2 to mark them.

[arshiya.g02]

I tried running FilterMutectCalls using the command : sudo ./gatk FilterMutectCalls -R /home/arshiya/efs/FastQC/hg38.fa -V /home/arshiya/efs/test/test_sample.vcf.gz -O /home/arshiya/efs/test/test_filter.vcf.gz

but it showed error like this : java.lang.IllegalArgumentException: log10 p: Values must be non-infinite and non-NAN at org.broadinstitute.hellbender.utils.NaturalLogUtils.logSumExp(NaturalLogUtils.java:84) at org.broadinstitute.hellbender.utils.NaturalLogUtils.normalizeLog(NaturalLogUtils.java:51) at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.clusterProbabilities(SomaticClusteringModel.java:203) at org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.learnAndClearAccumulatedData(SomaticClusteringModel.java:122) at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.learnParameters(Mutect2FilteringEngine.java:156) at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls.afterNthPass(FilterMutectCalls.java:151) at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:44) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1039) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205) at org.broadinstitute.hellbender.Main.main(Main.java:291)

[2nelly]

Which GATK version do you use? This seems to be a known reported bug.

[arshiya.g02]

Version GATK 4.1.2.0

[2nelly]

Sorry, for the delay I think these kind of bugs have been reported in 4.1 version. Try to use an older one like 4.0.11 or 4.0.12