We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

CalculateTargetCoverage error

yesitsjessyesitsjess Member
edited August 2017 in Ask the GATK team


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.


Sign In or Register to comment.