Tagged with #allelebalancebysample
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I am struggling with adding AlleleBalanceBySample and StrandBiasBySample to my joint VCF file. The data through joint VCF were generated with GATK 3.2-2, and I have tried using the VariantAnnotator as well as repeating the GenotypeGVCF step specifying the annotations. I have also tried using the GenotypeGVCFs tool from 3.3-0, but am trying to avoid running the HC again in the interest of time. For the strand bias by sample I can see why the VariantAnnotator approach would fail, as the information is not contained in the joint VCF file, but it is there in the GVCF. For the allele balance by sample it seems the info is already in the joint VCF, so either VariantAnnotation or rerunning GenotypeGVCFs seem like they should work.

I should add that when I do try to add these annotations using GenotypeGVCFs, they are noted in the header ##FORMAT section, but not in the actual F:O:R:M:A:T.

Any clues or hints (or admonitions!) much appreciated.


Comments (10)

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.

Comments (7)

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

Comments (3)


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?

Best wishes,