For the below vcf record, first sample is G/G (1/1-Heterozygous alternate) with allele depth of 101 reads. Whereas for the second sample is also G/G(1/1) with allele depth of 1 read. Overall depth is 102. If I filter vcf records base on DP >10. Then I will get this vcf record. But the second sample has only one 1 supporting read.
1) For multisample VCF, should I filter the variants based on allele depth (AD) or Overall depth (DP)?
2) What is VQSRTrancheBOTH99.00to99.90 (it is present in filter column)?