Entering edit mode
2.1 years ago
wang.yiguan ▴ 10
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!
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?
Yes, I've tried to remove
-A StrandBiasBySample, but still no
SBannotation in the output vcf.