Hi there!
I was trying to use the GATK 3.8 tool called GCContentByInterval, but I'm having a bit of trouble figuring what it is in my syntax that I'm getting wrong. I'm following the steps described in the XHMM tutorial, but for some reason GATK is not taking any input from me.
This is what I've tried so far:
java -Xmx1024m -jar $GATK -T GCContentByInterval -L /path/to/20120518.exome.consensus.chrom20.nochr.bed -R /path/to/human_g1k_v37.fasta -o DATA.GBR.locus_GC.txt
It doesn't help that the only error detected by the package is that it's unable to find the walker tool, which apparently is the standard error for just any error.
This is what the log looks like:
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: GCContentByInterval
ERROR ------------------------------------------------------------------------------------------
Could it be possible that this is about my interval list being a BED file? I used before the DepthOfCoverage tool, and it didn't have any problem with these files. I already have the reference index and dictionary along with the fasta file.
Any help or theories are deeply appreciated.
B.
