TYPE=Complex #189
Description
--Hi,
i have a question regarding the type Complex i have found in my analysis (vcf line below).
In this type of mutation i can't find how to calculate the VAF, it's strange because i have 390 alternate reads and 117 total reads,
how is it possible ?
And also i don't have the SVLEN field.
thank you for your help.
chr2 201258150 . CACAGGTTCTCCTCCTTTTATCTTTTGTGTTTTTTTTCAAGCCCTGCTGAATTTGCTAGTCAACTCAACAGGAAGTGAGGCCATGGAGGGAGGCAGAAGAGCCAGGGTGGTTATTGA G 252 PASS SAMPLE=abT_stSeq_005;TYPE=Complex;DP=117;VD=390;AF=1;BIAS=1:2;REFBIAS=113:3;VARBIAS=218:172;PMEAN=36.4;PSTD=1;QUAL=29.3;QSTD=1;SBF=0;ODDRATIO=29.5946;MQ=60;SN=96.5;HIAF=0.7705;ADJAF=1;SHIFT3=0;MSI=4;MSILEN=1;NM=0.3;HICNT=386;HICOV=501;LSEQ=CTGCTGGAGGGAAGTGTTTT;RSEQ=AAGTAAAAGAAACTTCTTCC;DUPRATE=0;SPLITREAD=284;SPANPAIR=2;CALLER=VarDict GT:DP:VD:AD:AF:RD:ALD 1/1:117:390:116,390:1:113,3:218,172