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GATK 4 version still have some problems with asterisk in the VCF files.
Dear GATK team,
I had used GATK 4 and GATK 3 best proctices to run WES data. BAM->gvcf->joint variant detection, VCF file->VQSR and so on.
I noticed that in the GATK offical website, you indeed had explained what * asterisk standed for. Right now, many people had tried to perform SelectVariants --selectTypeToExclude SYMBOLIC --excludeNonVariants --removeUnusedAlternates to remove * sign. I also had tried both GATK 4 and GATK 3. The above commands did not work at all.
for example, chr1 1296543 rs113960113 AACAC A,* 59000.80 . . GT:AD:DP:GQ:PL 0/0 0/2 0/0 0/1
My question is that GATK will treat this variant as mulitivariants, so it will be deleted when we do downstream analyses since we cannot retrieve or know what exactly genotype these sample have. Normally, if a unknown variant or panning deletion/insertion occures in this loci, we should not trust this variant. However, sometime, we indeed saw some these kind of variants had a pretty high quality. It will be pity to remove them or cannot retrieve them. Do you have any sugguestions about this? Many thanks.
chr1 1296543 rs113960113 AACAC A,* 59000.80 . . GT:AD:DP:GQ:PL 0/0 0/2 0/0 0/1