For the GRCh38 v4 structural variants, can we get a BED file similar to the one provided for GRCh37 v2 structural variants? Then we could use our existing track build procedures to have a track at UCSC too.
Thanks,
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What is the link for the v4.1 cnv and sv bed files? This page says they exist:
Alternatively, the gnomad GitHub repo contains a script that looks as if it converts VCF to BED. Can we use that ?
@gnomad_council @Kaitlin_Samocha We work for the UCSC Genome Browser and need to make the Gnomad SV track soon. This question has been sitting here for a month, we need this to move forward. Can someone give us an idea if or how we can run your VCF->BED converter? The issue is that other resources need to display the SV dataset and if every resource displays it in a different way, that’s not ideal. We’d like to the keep the new display (so the BED) similar to the old data. You used to provide BED format, but don’t anymore, so we’ll have to decide how we show the VCF now. It’s possible that this is an easy conversion, but if we do this ourselves, we may come up with different ways to display these SVs than what you did in the previous version. If you are not supporting BED conversion anymore, that’s OK, too, but it would be good to know before we come up with a SV display converter ourselves. I think it would be good if Gnomad provides the BED data again, so the various browsers don’t all have to come up with possibly different ways to show the SVs… Thanks!
Hi all,
Thank you for the inquiry and for following up. We are a small team with limited bandwidth, and we try to answer inquiries where we can.
The v4.1 SV BED files are now available for download in our public buckets but are not yet linked on the Downloads page. The team will work on adding the links in the near future, but for now, here are the links to download them from GCP:
Great, many thanks!! This should mean that we’ll have the tracks up very soon!
Thank you for making the v4.1 SV BED files available for download. We did notice that the v4.1 CNV data is not available in BED format.: gnomAD
Could we also get the v4.1 CNV data in BED format?
Thank you for providing these!
I noticed the header of the sv bed file has 626 fields while the rows have 625. I am considering tabs as field separators and there is no trailing whitespace in the header. Is this an error?
Hi! Have you encountered a problem with the header having 1 more field than the data rows? How did you resolve this? Thank you!
Can you clarify how you’re parsing this file? I’m seeing a consistent number of fields between the header and data (626 fields in both)
Thanks for your quick reply. When I use awk to count the number of fields and specify a tab delimitor, I get 626. When I don’t specify the delimitor, I get 625 in the data rows. This is causing some issues with other tools where I get an error of not enough data fields based on what is expected from the header.
Hi! Following up about this issue. I’m using AnnotSV with custom bed annotations and it is giving an error because I cannot specify tab delimitors for the inputted bed file. I’ve looked at the file and don’t see any extra tabs or spaces. I’m not sure how to work around this. Do you have any suggestions?