VariantFiltration applied to mutect calls generates substantially different FA in some cases?

lintnerlintner Cambridge, MAMember, Broadie

Hi Folks,
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.

Any ideas?

Thanks,
Robert

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