issue in the vcf format using Mutect2
1
0
Entering edit mode
3.2 years ago
arshiya.g02 ▴ 10

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

next-gen • 1.7k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Anbody know why most POPAF=7.3?

ADD REPLY
0
Entering edit mode
3.2 years ago
2nelly ▴ 310

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.

ADD COMMENT
0
Entering edit mode

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)

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Version GATK 4.1.2.0

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1285 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6