Not every line was annotated?

[xiucz]

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

[brentp]

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.

[xiucz]

@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