Dear all,
we have been sequencing pediatric tumors by using Illumina technology (normal-tumor pairs, paired end reads of 150nt each), and I have been using several SV callers (including DELLY, MANTA, LUMPY) in order to call the Structural Variants.
Considering the initial files of SV calls, what is the set of criteria you would recommend for filtering ? particularly, the number of PR (paired-end reads) or SR (split - reads) ? thank you,
-- bogdan
Dear Daniel, took a quick look in your paper and it looks fascinating : GRIDSS is among the first algorithms, that combines assembly, SR and PR analysis. Wondering how extensive have you tested it in on cancer samples, for somatic SV detection. We can also take the conversation via email, if you'd like. Thanks.