Question about vcf INFO filed

[hyunjokoo]

Hello,

This is the result vcf file of Sniffles2. ctg001060 2711 Sniffles2.DEL.23S1 a N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=-1;END=2712;SUPPORT=3;COVERAGE=4,6,6,6,6;STRAND=-;AF=0.500;STDEV_LEN=0.000;STDEV_POS=0.000 GT:GQ:DR:DV 0/1:21:3:3

And this is the result vcf file of CuteSV. ctg000650 159298 cuteSV.INS.28 C CTAGATCACGATCCGTCACCCCCACTCCTGT . PASS PRECISE;SVTYPE=INS;SVLEN=30;END=159298;CIPOS=-0,0;CILEN=-0,0;RE=23;RNAMES=NULL GT:DR:DV:PL:GQ ./.:.:23:.,.,.:.

I would like to know how many reads support this vaiant. In Sniffles2, SUPPORT=3 is what I want. Which represents the supporting read number in CuteSV? I think RE is that one, but I could not find what RE means.

Could you please also explain what CIPOS, CILEN and RNAMES stand for?

Thank you. HJK

[Meltpinkg]

Hello, @hyunjokoo

The representation of the INFO fields are provided in the header of the VCF file, and the details are listed below: RE represents the number of read support the SV record. CIPOS / CILEN represents the confidence interval of the breakpoint/SV length of the SV record, respectively. RNAMES represents the read names of the read support the SV record. This field is only reported when running commands with report_readid.

Best, Shuqi