I am using gatk 18.104.22.168
I called gcvf for each sample using
gatk HaplotypeCaller -ERC GVCF -A StrandBiasBySample
SB information is present in gvcf, but when I called genotype using GenotypeGVCFs,
the SB information is gone from the vcf.
I tried to fix it by adding -A StrandBiasBySample
Then I get this error
WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
And still no SB in the output format.
I wonder how to fix it.
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