Open zhemingfan opened 1 year ago
Thank you for sharing your experience.
I encountered the same issue where the Circos Plot could not be displayed in the SV inspector of jbrowser2 due to the following record:
chr7 61067874 d_338 T <INS> . Too_small_size END=61067865;SVTYPE=INS;SVINSLEN=14;SVINSSEQ=TGAATCAAATGGTG TR:VR 60:16 23:0
As shown in the screenshot below:
When I ran bcftools view tumor.nanomonsv.result.vcf
, I received the following warning message:
[W::vcf_parse_info] INFO/END=61067865 is smaller than POS at chr7:61067874
Thank you very much. These variants should be filtered due to the Too_small_size tags. However, I would like to develop a more general solution. These might be categorized as DUP or DUP:TANDEM instead of INS.
@friend1ws I've come across this too on a number of sites with v0.7.1. Several of them are not filtered for small size either.
OK. will try to solve in the next version.
Hi @friend1ws ,
I've noticed that in the final output we received a call similar to:
chr6 31427745 d_1188 A <INS> . Too_small_size END=31427708;SVTYPE=INS;SVINSLEN=0;SVINSSEQ= TR:VR 107:8 61:0
Is there a possibility to add a check to coerce the end positions to be equal or greater than the start position for insertions and deletions?Thanks