To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

[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


Best Answer


Sign In or Register to comment.