We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
[ERROR] GATK4 Mutect2
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 http://broadinstitute.github.io/picard/index.html#GettingHelp 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(AbstractVCFCodec.java:281) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:262) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:64) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:70) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:37) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:372) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:353) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:314) at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71) at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57) at htsjdk.samtools.util.MergingIterator.next(MergingIterator.java:107) at picard.vcf.MergeVcfs.doWork(MergeVcfs.java:221) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:269) at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:24) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:153) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195) at org.broadinstitute.hellbender.Main.main(Main.java:277)
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