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VariantFiltration applied to mutect calls generates substantially different FA in some cases?
I'm using Mutect to call somatic variants on some human gene panel data (~660 amplicons). After making the calls I applied VariantFiltration in order to limit the variants to a specific set of coordinates (via a bed file). VariantFiltration seems to have done the job in terms of selecting the correct regions; however, the FA can be quite different, but not always.
For example (HOT = VariantFiltration Applied): 3 samples
[sample name = c2; FA = c15]
HOT ras119 12 25360224 rs61764370 A C KRAS 0/1 853 38 24 891 0.043 4.3
FULL ras119 12 25360224 rs61764370 A C KRAS 0/1 584 290 28 878 0.332 33.20
HOT ras116 12 25360224 rs61764370 A C KRAS 0/1 536 345 25 884 0.392 39.2
FULL ras116 12 25360224 rs61764370 A C KRAS 0/1 447 405 27 854 0.475 47.50
HOT ras25 12 25360224 rs61764370 A C KRAS 0/1 833 97 25 930 0.104 10.4
FULL ras25 12 25360224 rs61764370 A C KRAS 0/1 638 236 28 876 0.27 27.00
It isn't clear to me why this would change, nor is it clear which number I should believe.