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.
Sorry - I'm very inexperienced at this. I'm trying to follow this documentation:
I was a little unclear on what to use as the target file, so I've downloaded the following from SureDesign:
Agilent SureSelect DNA - SureSelect Human All Exon V6 r2 - Covered bed file extended by 100bp on either side
This is the command I'm using:
software/bioinf/gatk_v4/gatk-launch CalculateTargetCoverage -I hg19.chronly.alignment.bam -T S07604514_Padded.bed -transform PCOV -groupBy SAMPLE -targetInfo FULL –keepdups -O /test.pcov
Then I got:
A USER ERROR has occurred: Invalid argument '–keepdups'
So removed that, then:
17:01:02.317 INFO CalculateTargetCoverage - HTSJDK Defaults.COMPRESSION_LEVEL : 1
17:01:02.317 INFO CalculateTargetCoverage - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:01:02.317 INFO CalculateTargetCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:01:02.317 INFO CalculateTargetCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:01:02.317 INFO CalculateTargetCoverage - Deflater: IntelDeflater
17:01:02.317 INFO CalculateTargetCoverage - Inflater: IntelInflater
17:01:02.317 INFO CalculateTargetCoverage - Initializing engine
17:01:02.665 INFO CalculateTargetCoverage - Done initializing engine
17:01:02.671 INFO CalculateTargetCoverage - Reading targets locations from intervals...
17:01:02.673 INFO CalculateTargetCoverage - Reading target intervals from targets file 'S07604514_Padded.bed' ...
17:01:02.674 INFO TargetTableReader - Reading targets from 'S07604514_Padded.bed' ...
17:01:02.678 INFO CalculateTargetCoverage - Shutting down engine
[02 August 2017 17:01:02 BST] org.broadinstitute.hellbender.tools.exome.CalculateTargetCoverage done. Elapsed time: 0.01 minutes.
A USER ERROR has occurred: Bad input: format error at line 1: Bad header in file. Not all mandatory columns are present. Missing: stop, name, start, contig
Use -DGATK_STACKTRACE_ON_USER_EXCEPTIONto print the stack trace.