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[ERROR] GATK4 Mutect2

cbaocbao Member, Broadie


I want to call mutations for my WGS data. But, the workflow for one of my pairs is failed. I got the following ERROR message in MergeVcfs task. It seems that one of the VCF files is not in correct format. But, I checked it and did not find any format issue. Could you please help me? Thanks a lot!

Workspace ID: 8d717792-41af-4339-ac2b-634540370e63
Submission ID: 26cd48f6-5815-4472-a185-c9e38b2fa2c7

00:00:04s. Time for last 10,000: 0s. Last read position: 18:19,501,893 INFO 2018-02-20 19:36:15 MergeVcfs Processed 320,000 records. Elapsed time: 00:00:04s. Time for last 10,000: 0s. Last read position: 19:43,221,725 [Tue Feb 20 19:36:15 UTC 2018] picard.vcf.MergeVcfs done. Elapsed time: 0.08 minutes. Runtime.totalMemory()=886046720 To get help, see htsjdk.tribble.TribbleException: Line 5829: there aren't enough columns for line 20 57842652 . A AT . . DP=68;ECNT=1;NLOD=3.53;N_ART_LOD=1.58;P (we expected 9 tokens, and saw 8 ), for input source: file:///cromwell_root/fc-8d717792-41af-4339-ac2b-634540370e63/26cd48f6-5815-4472-a185-c9e38b2fa2c7/Mutect2/27df3a6c-a00c-4cd0-a3e3-81ff18676b25/call-M2/shard-45/output.vcf.gz at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine( at htsjdk.variant.vcf.AbstractVCFCodec.decode( at htsjdk.variant.vcf.AbstractVCFCodec.decode( at htsjdk.tribble.AsciiFeatureCodec.decode( at htsjdk.tribble.AsciiFeatureCodec.decode( at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord( at htsjdk.tribble.TribbleIndexedFeatureReader$ at htsjdk.tribble.TribbleIndexedFeatureReader$ at htsjdk.samtools.util.PeekableIterator.advance( at at at picard.vcf.MergeVcfs.doWork( at picard.cmdline.CommandLineProgram.instanceMain( at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain( at org.broadinstitute.hellbender.Main.runCommandLineProgram( at org.broadinstitute.hellbender.Main.mainEntry( at org.broadinstitute.hellbender.Main.main(

The line:
20 57842652 . A AT . . DP=68;ECNT=1;NLOD=3.53;N_ART_LOD=1.58;POP_AF=1.000e-03;P_GERMLINE=-2.786e+00;RPA=11,12;RU=T;STR;TLOD=3.44 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:24,3:0.206:9,2:13,1:24:272,216:60:33:0.111,0.00,0.111:7.290e-03,0.069,0.923 0/0:28,2:0.116:17,1:9,1:29:245,231:60:48


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