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From: Steven R. <sr...@fo...> - 2019-11-03 00:11:57
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Hi, For “readability” we were looking at representing largish deletions (say > 1kb) in VCF using the symbolic key approach illustrated in the VCF docs for a simple deletion when treated as a structural variant – using a “<DEL>” symbolic key for example. But I had two questions. First, consider a “simple” deletion which I represent below two alternative ways. Although this is a small deletion for illustration and we would use the first approach, we would consider the second approach for a much larger deletion. #CHROM POS ID REF ALT QUAL FILTER INFO 2 100 . TACT T 30 PASS SVTYPE=DEL;END=103;SVLEN=-3 2 100 . T <DEL> 30 PASS SVTYPE=DEL;END=103;SVLEN=-3 But what about a similar but “complex” deletion, where the ACT sequence is deleted but a G inserted. #CHROM POS ID REF ALT QUAL FILTER INFO 2 101 . ACT G 30 PASS SVTYPE=DEL;END=103;SVLEN=-2 First, is SVLEN -2 (len(alt)-len(ref)) or -3 (end-pos+1)? The docs would seem to suggest the former (-2), a net change in length rather than the number of reference bases involved, but wanted to confirm. Second, how would you represent this using the symbolic key approach? (Again, illustrating using this short variant, but it would only be of interest for a larger event.) Using the approach illustrated for a simple deletion places the “<DEL>” string in the ALT field, meaning the ALT=G is unspecified. #CHROM POS ID REF ALT QUAL FILTER INFO 2 101 . A <DEL> 30 PASS SVTYPE=DEL;END=103;SVLEN=-2 Alternatively, one could imagine putting “<DEL>” in the REF fields instead: #CHROM POS ID REF ALT QUAL FILTER INFO 2 101 . <DEL> G 30 PASS SVTYPE=DEL;END=103;SVLEN=-2 This permits the alt alelle(s) to be specified, but the examples in the v4.3 spec never use a symbolic reference in the “REF” field. Thanks. This communication and any files transmitted with it may contain information that is considered to be confidential, privileged and exempt from disclosure under applicable law. This message is intended for Foundation Medicine-affiliated use and that of the intended recipient only and may contain information that is protected by Foundation Medicine policies and the HIPAA Privacy Rule, 45 CFR § 164.500. This communication is intended solely for the use of intended recipient. If you are not the intended recipient, you are hereby notified that any use, dissemination or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete this message immediately. Thank you for your cooperation. |