GATK no "SB" annotation after GenotypeGVCFs

Question

[wang.yiguan]

Hi,

I run the following command to generate a gvcf file.

gatk HaplotypeCaller -R dmel-all-chromosome-r6.36.fasta \
    -I sample_43.sort.noDup.realign.bam \
    -ERC GVCF \
    -L 4 \
    -O sample_43_chr4_test.g.vcf.gz

This gvcf file contains the StrandBiasBySample or SB annotation. And then I run GenotypeGVCFs as following:

gatk GenotypeGVCFs -R dmel-all-chromosome-r6.36.fasta \
    -V sample_43__chr4_test.g.vcf.gz \
    -A StrandBiasBySample \
    -O sample_43_chr4_test.vcf.gz

The SB annotation disappeared in the final output vcf file sample_43_chr4_test.vcf.gz ! I want to keep the SB annotation in the final vcf.

I was trying to google a solution, but failed.

Thanks in advance!

[desouzareis.r]

Hi,

There is a post on GATK forum that may help: Missing annotations in the output callset VCF.

Have you tried to remove the "-A StrandBiasBySample" option from your GenotypeGVCFs command?

[wang.yiguan]

Yes, I've tried to remove -A StrandBiasBySample, but still no SB annotation in the output vcf.