happy new year ! talking about the calling of SV (Structural Variants) in cancer samples, and about the SOMATIC AF (allele fractions) for DEL, INS, DUP, TRA, INV in CANCER SAMPLES :
what is the formula that is used when computing SOMATIC AF ?
is it the RATIO of A) PR (paired reads) + SR (split reads) supporting the SV in cancer samples, versus B) TOTAL PR (paired reads) + SR (split reads) that are spanning across the break point ?
or any other formula that is used ?
and, when we do more stringent filtering of SV, what is the minimal number of PR and SR we shall use ? thank you,