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SelectVariants According to AD Values
How can I select variants that has specific AD values?
Since AD parameter has two values (reference depth, allele depth) I couln't find that how can I write related expression on script. If I wanted to select variants that their allele depth is greater 100, which expression should I use? (e.g "AD > 100 ?)
Also, several times I came across inconsistencies between AF values and AD values. In the example below, AD values show that there is 69 reference and 78 allele depth. It should indicate about 0.53 AF. However, UnifiedGenotyper gives its AF as 1.00. What could be the reason og that situtation?
CM001522.1 69914 . T C 2657 . AC=1;AF=1.00;AN=1;BaseQRankSum=3.287;DP=147;Dels=0.00;FS=12.559;HaplotypeScore=94.3377;MLEAC=1;MLEAF=1.00;MQ=41.70;MQ0=41;MQRankSum=4.393;QD=18.07;ReadPosRankSum=1.197;SOR=4.017 GT:AD:DP:GQ:PL 1:69,78:147:99:2687,0