GATK no "SB" annotation after GenotypeGVCFs
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
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
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!
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