computing the AF (allele fraction) for SV

Question

[Bogdan]

Dear all,

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,

-- bogdan

[Kevin Blighe]

I can only imagine that you are referring to SVs in a VCF file? If so, then AF should be allele frequency and relate, therefore, to AF for all other variant types. It may be different depending on which program you used, though (?).

[Bogdan]

Thanks Kevin. I.ve been using DELLY and LUMPY, and here 've found a piece of literature that offered more info : https://scholarship.rice.edu/bitstream/handle/1911/87870/FAN-DOCUMENT-2015.pdf

[Kevin Blighe]

Umm... I may attempt to read that on my next long-haul flight...

[Bogdan]

eheee ... happy reading !