-DepthOfCoverage-ct not working in GATK 4.1.8.1
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.1.8.1
b) Exact command used: java -jar gatk-package-4.1.8.1-local.jar DepthOfCoverage -R ucsc.hg19.fasta -I 1.bam -O 1_pregatk_base -L 2.bed -ct 125 >& depthofcoverage.log
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):
I'd like to get the percent of reads under the threshold using -ct or -summary-coverage-threashold as I did in previous version.
Thanks!
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Wei you can see the updated parameters available in GATK4 at the DepthofCoverage documentation page: https://gatk.broadinstitute.org/hc/en-us/articles/360046789152-DepthOfCoverage-BETA-
Please also make note of the recommended command line syntax and use the GATK wrapper script because if you run GATK4 as you have above, you may run into strange issues: https://gatk.broadinstitute.org/hc/en-us/articles/360035531892-GATK4-command-line-syntax
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java -jar gatk-package-4.1.8.1-local.jar DepthOfCoverage -R ucsc.hg19.fasta -I 1..bam -O pregatk_base -L my.bed -ct 125 >& ct.log
A USER ERROR has occurred: c is not a recognized option
If I ran the wrapper gatk directly, it looked for python (python 3.*) at /usr/bin/env: ‘python’: No such file or directory
while we have python 2 as default. -
Wei please read the article I sent about DepthofCoverage options, -ct is not an option in GATK anymore.
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Which older version still has it? Or which option is equivalent to that?
Thanks!
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-ct was an option in GATK3, which we do not provide support for any longer. Read the tool docs that I sent you for recommended usage for the newest version of DepthofCoverage, which we recommend using.
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