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Published 20 hours ago • verified publisher icon fritzsedlazeck

Inconsistency:Insertion variants length different in the ALT column with sv len.

Open infotmatician opened this issue 2 years ago • 2 comments

Hi, Hope you are doing well. For some records in insertion variants are inconsistent with their ALT column sequences between SV_LEN. As an example; 1 249239182 Sniffles2.INS.5B7ES0 N GCGTCGCCTCTCTCATGTCAGCGCCATGCGCCGCGCCTCTGCGCCTGGGCGCCGCGCGCCGTCGCCCCATGCTCATGCCAAGGCCACACATGCTTCTCTCTGCGCCTGCGCGCGCCGCGCCCTCTGCGCCTGGGCGCCGCGCGCCGCGCCCTCTGCGCCCCTGGGT 54 PASS IMPRECISE;SVTYPE=INS;SVLEN=203;END=249239182;SUPPORT=92;COVERAGE=81,75,75,75,71;STRAND=+-;AF=1.000;STDEV_LEN=50.745;STDEV_POS=26.711;SUPPORT_LONG=0 GT:GQ:DR:DV 1/1:60:0:92

Inserted sequences that present on the ALT column is 166, but in the info column SV_LEN=203. Which one is the actual insertion length? Should I trust Inserted sequences on ALT column for my research? BEST

infotmatician avatar Dec 02 '22 12:12 infotmatician

Thanks for pointing this out. We are running a consensuse sequence algorithm on top of the read estimations.. I would suspect that the discordance comes from this. I will mark that as it shuold get fixed. Thanks Fritz

fritzsedlazeck avatar Dec 02 '22 13:12 fritzsedlazeck

Hi Can you tell me where to check the filter commands and conditions of the sniffles software? I am waiting for your reply. Best wishes for you. Sincerely Yours, Zhao Yajun

yajun1314 avatar Jan 13 '23 02:01 yajun1314