search

mroosmalen / nanosv

SV caller for nanopore data
MIT License
90 stars 22 forks source link

DR and DV fields on VCF #69

Closed dangeles closed 4 years ago

dangeles commented 4 years ago

Hi!

I used nanosv for a structural variant project and it works very nicely. However, I am having issues making sense of the DR and DV fields. I know DV and DR are tuples, but I cannot understand whether the tuples represent (total, forward) or (forward, reverse) reads or something else.

Below are three entries that lead to some of my confusion:

chr1 | 261535908 | 1298477 | A | [CHR12:25386214[A | 125 | PASS | IMPRECISE;SVTYPE=BND;SVMETHOD=NanoSV_v1.2.4;CI... | GT:DR:DV:GQ:HR:PL | 0/1:8,4:3,3:68:0,0:125,0,68

In the above entry, DR = 8,4. 8 is the number of reads in the Ref Read ID field.

In a second entry, from the same analysis

chr1 | 81711589 | 1424026 | A | [CHR15:68078428[A | 35 | PASS | IMPRECISE;SVTYPE=BND;SVMETHOD=NanoSV_v1.2.4;CI... | GT:DR:DV:GQ:HR:PL | 0/1:5,19:2,2:35:0,0:35,0,157

Here, DR=5,19, and 5 is the number of reads in the Ref Reads ID field.

Finally, a third entry, from the same analysis:

chr11 | 57647898 | 1489859 | T | T[CHR14:78022342[ | 32 | PASS | SVTYPE=BND;SVMETHOD=NanoSV_v1.2.4;CIPOS=0,0;CI... | GT:DR:DV:GQ:HR:PL | 0/1:5,20:2,2:32:0,0:32,0,164

Here, DR=5,20, and 20 is the number of reads in the Ref Reads ID field.

Any chance you could help me out? I would really appreciate it!

Best, David