Confirming a gatk command in XBS_call

[abhi18av]

Hi @TimHHH ,

Is the following command correct?

 $JAVA -Xmx64G -jar $GATK -V PREFIX.potentialSV.vcf.gz -O PREFIX.potentialSV.DRgenes.vcf.gz -XL $RESOURCE_PATH/DRgenes.list

In the original codebase this is commented out at XBS_call Line-140.

I'm confirming this since gatk TOOL isn't mentioned, only the -V and -XL sub-options are used in the code.

-V is same as --variant
-XL is same as --exclude-intervals

Reference:
https://gatk.broadinstitute.org/hc/en-us/articles/360036510892-VariantRecalibrator

[TimHHH]

Well spotted.
It should be:
$JAVA -Xmx64G -jar $GATK SelectVariants -V PREFIX.potentialSV.vcf.gz -O PREFIX.potentialSV.DRgenes.vcf.gz -L $RESOURCE_PATH/DRgenes.list
Also note the -L rather than the -XL.

[abhi18av]

Ah, okay. Thanks Tim!