Weird parameter of Depth of coverage (GATK4.1.7.0 beta version)
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: gatk-4.1.7.0
b) Exact command used:
java -Xmx25g -jar /garnet/Tools/WGS_Analysis/Program/GATK/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar DepthOfCoverage -R /garnet/Tools/WGS_Analysis/DB_Analy/iSAAC/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -I Free_550_2_2.recal.bam -O ./new/Free_550_2_2.recal.depcov -ct 1 -ct 2 -ct 5 -ct 10 -ct 15 -ct 20 -ct 30 -ct 40 -ct 50 -L /garnet/Tools/WGS_Analysis/DB_Analy/iSAAC/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/Homosapiens_hg19.bed --omit-depth-output-at-each-base true --omit-interval-statistics true
c) Entire error log:
***********************************************************************
A USER ERROR has occurred: c is not a recognized option
***********************************************************************
If not an error, choose a category for your question(REQUIRED):
c) Why do I see (these error message)?
In GATK4 beta manual page, We found these parameter usage in depth of coverage.....
When I tried to use above command, I got an error message.
As you can see my command line, I could not type the 'c' option.
But, if I tired to command without "-ct option", it worked well.
Could you give me some advice about this problem?
Thank you,
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I solved this problem by using --summary-coverage-threshold option instead '-ct' like this
"--summary-coverage-threshold 1 --summary-coverage-threshold 2 --summary-coverage-threshold 5 --summary-coverage-threshold 10 ..."
I remain this post for other people who suffer the same issue.
Thank you,
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Hi Henry, thanks for bringing this to our attention. The usage example is out of date and we will get that documentation changed in the next GATK release.
The -ct argument is an old argument from GATK3 and is now --summary-coverage-threshold.
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