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.