I've got HaplotypeCaller working nicely in standard mode, like so:
# Run haplotypcaller
gatk --java-options "-Xmx4g" HaplotypeCaller \
--intervals "$INTERVALS" \
-R "$REF" \
-I "$OUT"/results/alignment/${SN}_sorted_marked_recalibrated.bam \
-O "$OUT"/results/variants/${SN}_g.vcf.gz \
-ERC GVCF
But when I try in allele-specific mode, I get the following error. All I've done is add the -G annotations at the end, as suggested here.
# Haplytype caller with allele-specific annotations
gatk --java-options "-Xmx4g" HaplotypeCaller \
--intervals "$INTERVALS" \
-R "$REF" \
-I "$OUT"/results/alignment/${SN}_sorted_marked_recalibrated.bam \
-O "$OUT"/results/variants/${SN}_g.vcf.gz \
-ERC GVCF \
-G Standard \
-G AS_Standard
Here's the error:
***********************************************************************
A USER ERROR has occurred: Unrecognized annotation group name: Standard
***********************************************************************
I think that those options should be: -G StandardAnnotation
-G AS_StandardAnnotation
At least, when I changed them to that, it didn't throw an error message.
However, I haven't used GATK much, so I'm not sure that's correct. I posted on the relevant Broad page, so more info may show up there.