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Not every line was annotated?
Hi,
I use duphold to calculate SV depth, but I find that not every vcf line was annotated with the tags, how to interpret this situation?
chr17 57986589 7_2 N [chr17:41256075[N 0 . SVTYPE=BND;STRANDS=--:8;IMPRECISE;CIPOS=-237,5;CIEND=-207,9;CIPOS95=-48,1;CIEND95=-29,3;MATEID=7_1;EVENT=7;SECONDARY;SU=8;PE=8;SR=0;GCF=0.437831 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB:DHFC:DHFFC:DHBFC ./.:8:8:0:.:.:.:0:0:0:0:0:0:0:0:0:0:.:0:0:0
chr17 59934382 9_2 N ]chr1:59536384]N 0 . SVTYPE=BND;STRANDS=-+:4;CIPOS=-9,8;CIEND=-9,8;CIPOS95=0,0;CIEND95=0,0;MATEID=9_1;EVENT=9;SECONDARY;SU=4;PE=0;SR=4 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB ./.:4:0:4:.:.:.:0:0:0:0:0:0:0:0:0:0:.
Best, xiucz
Duphold doesn't annotate every BND, if the end is close enough it will. In this case, it looks like there were 0 reads with sufficient quality to evaluate the depth.
@brentp
Thanks for your quick reply, what does the the end is close enough
mean?
And one more question, the three tags, DHFC, DHFFC, DHBFC, which one refers to the VAF value? Thank you.
best, xiucz