Loss of RSIDs for GenotypeGVCFs, possibly an issue with dpsnp filter.vcf file from SelectVariants
I've run into this problem a few times now having attempted to debug the issue in various ways. The first time it occurred I was using a vcf file containing the rsids I wished to genotype on a given gvcf file. There was no error message that I could discern, however the resultant vcf file only contained <1/5th of the rsids of interest in the filter file.
I assumed this issue related to the gvcf file and so acquired the bam file to begin the workflow from the beginning and stick to best practices, however I have now run into the same issue using haplotype caller and the same filter.vcf file as the -L and -D argument.
This leads me to believe the filter file is the issue, but when I look at the file I can see all of the rsids there so I'm not sure what is causing the loss. Of lesser concern is the loss of 7 rsids when I used SelectVariants to produce the filter initially, but I will also have to address that.
I have attempted to reduce the minimum base quality reads to 1 but it has not resulted in any increase in variant calling. I also looked into generating a bamout file which I will return to when possible, however I am currently working remotely and unable to install IGV on this device.
Many thanks for any tips