Using GATK 3.1-1, I seem to be unable to get the "AB" (AlleleBalance) annotation for the calls using the HaplotypeCaller -> GenotypeGVCFs pipeline, and I'm not sure how to get it. Our current pipeline (GATK 2.7-4, UnifiedGenotyper) requires this field to perform filtering, so this annotation is essential for us to upgrade to GATK 3.1.
My current pipeline of commands is as follows:
$ GenomeAnalysisTK-3.1-1 -T HaplotypeCaller -R human_g1k_v37_decoy.fasta --dbsnp dbsnp_137.b37.vcf.gz -I
$ GenomeAnalysisTK-3.1-1 -T GenotypeGVCFs -R human_g1k_v37_decoy.fasta --dbsnp dbsnp_137.b37.vcf.gz -V
Above, note that if "-A AlleleBalance" is given to GenotypeGVCFs, GATK crashes with a NullPointerException (AlleleBalance.java, line 66).
The command above is heavily adapted from the current pipeline; do you know what I might be doing wrong with the new and improved HaplotypeCaller?
Thanks so much for your help, and if you need any further information, please let me know.
Version 3.1.1. Human normal samples.
I couldnt find AlleleBalance and AlleleBalanceBySample tags in my vcf outputs. Tags are not found even for single variant I tried HaplotypeCaller with -all or directly with -A AlleleBalance or -A AlleleBalanceBySample. Also I tried Variantannotator with -all or -A AlleleBalance or -A AlleleBalanceBySample.
Any help will be apreciated
I would like to filter my variants using the SelectVariants walker but it throws an error when I try to filter on allele balance by sample. The jexl expression I use is:
error is: unknown, ambiguous or inaccessible method getAB
Is there any way of filtering on this parameter?