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Obtaining the "AB" information from HaplotypeCaller and GVCFs
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 -L targets.GRCh37.bed -stand_emit_conf 10 -mbq 20 --downsample_to_coverage 300 -ERC GVCF -pairHMM VECTOR_LOGLESS_CACHING -variant_index_type LINEAR -variant_index_parameter 128000 -A HaplotypeScore -A MappingQualityRankSumTest -A ReadPosRankSumTest -A FisherStrand -A GCContent -A AlleleBalanceBySample -A AlleleBalance -A QualByDepth -o sample_gvcf.vcf.gz
$ GenomeAnalysisTK-3.1-1 -T GenotypeGVCFs -R human_g1k_v37_decoy.fasta --dbsnp dbsnp_137.b37.vcf.gz -V -L targets.GRCh37.bed -A QualByDepth -A HaplotypeScore -A MappingQualityRankSumTest -A ReadPosRankSumTest -A FisherStrand -A GCContent -A AlleleBalanceBySample -o joint_vcf.vcf.gz
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.