Question: computing the AF (allele fraction) for SV
1
gravatar for Bogdan
15 days ago by
Bogdan340
Palo Alto, CA, USA
Bogdan340 wrote:

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

ADD COMMENTlink modified 12 days ago by Biostar ♦♦ 20 • written 15 days ago by Bogdan340

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 (?).

ADD REPLYlink written 14 days ago by Kevin Blighe11k

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

ADD REPLYlink modified 14 days ago • written 14 days ago by Bogdan340

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

ADD REPLYlink written 14 days ago by Kevin Blighe11k
1

eheee ... happy reading !

ADD REPLYlink written 14 days ago by Bogdan340
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