The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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