Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!
Values for QD annotation not detected for ANY training variant in the input callset.
I am running VariantRecalibrator on 2 WGS using the command:
gatk VariantRecalibrator \
-R ./hg38/Homo_sapiens_assembly38.fasta \
-V combinedgVCF.g.vcf.gz \
--resource hapmap,known=false,training=true,truth=true,prior=15.0:./hg38/hapmap_3.3.hg38.vcf.gz \
--resource omni,known=false,training=true,truth=false,prior=12.0:./hg38/1000G_omni2.5.hg38.vcf.gz \
--resource 1000G,known=false,training=true,truth=false,prior=10.0:./hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
--resource dbsnp,known=true,training=false,truth=false,prior=2.0:./hg38/dbsnp_146.hg38.vcf.gz \
-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR \
-mode SNP \
--output /VQSR_test/output.recal \
--tranches-file /VQSR_test/output.tranches \
The combined GVCF of the 2 WGS is produced using: HaplotypeCaller -ERC GVCF -> CombineGCVFs -> GenotypeGVCFs
The QD, MQ, MQRankSum, ReadPosRankSum, FS and SOR scores are present in all the variant calls in the input gvcf.
Why is "Values for QD annotation not detected for ANY training variant in the input callset." when I can see that they are present in the input callset? What am I doing wrong here?
Also, the tranches file is empty.
Hope you can help.