Does the gatk/3.4-46 version (or older) have the option --excludeIDs?
I'm trying to use it but it keep giving the ERROR MESSAGE: Argument with name 'excludeIDs' isn't defined.
here the code I'm using:
java -Xmx60g -jar /cluster/software/VERSIONS/gatk-3.4-46/GenomeAnalysisTK.jar \
-R $REF \
-T SelectVariants \
-V $INPUT/SNPs_missInd_filtered.vcf \
--excludeIDs ex_list.txt \
Thanks for your help!