SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
bedtools - adding fields to bedpe files toadstools Bioinformatics 1 01-06-2017 12:42 PM
assembler outputs susanklein Bioinformatics 11 10-29-2014 01:37 AM
bamToBed bedpe oursu General 1 04-01-2014 04:54 AM
Dialign2-2 outputs RTK45 Bioinformatics 1 03-01-2012 02:39 AM
merging and de-duplicating structural variant calls (bedpe) splaisan Bioinformatics 0 06-27-2011 08:29 AM

Reply
 
Thread Tools
Old 03-29-2017, 03:03 AM   #1
2nelly
Junior Member
 
Location: switzerland

Join Date: Feb 2016
Posts: 7
Default SV vcf outputs to bedpe

Hi all,

Does anybody have scripts to convert:

breakdancer output ----> bedpe

delly vcf ---> bedpe

Thank you all in advance!!! cheers
2nelly is offline   Reply With Quote
Old 03-29-2017, 05:04 PM   #2
dcameron
Member
 
Location: Australia

Join Date: Mar 2013
Posts: 26
Default

It's not the cleanest approach for your purposes but you can do:

breakdancer->VCF using https://github.com/PapenfussLab/sv_b...kdancer2vcf.py

Then convert the VCFs (DELLY & BreakDancer) into R break-end GRanges object using https://github.com/PapenfussLab/Stru...iantAnnotation

Then convert the break-end GRanges to bedpe similar to how it is done in:

https://github.com/PapenfussLab/grid...mple/somatic.R

That said, I've found this approach quite powerful for SV analysis as you can perform annotation and filtering on the GRanges objects in R in just a few couple of code.

Last edited by dcameron; 03-29-2017 at 05:08 PM.
dcameron is offline   Reply With Quote
Old 03-30-2017, 06:44 AM   #3
2nelly
Junior Member
 
Location: switzerland

Join Date: Feb 2016
Posts: 7
Default

Thnx!

Actually, I tried a week ago the python script for breakdancer, but this is not what I was looking for.

By the way GRanges is a good approach
2nelly is offline   Reply With Quote
Old 03-30-2017, 04:27 PM   #4
dcameron
Member
 
Location: Australia

Join Date: Mar 2013
Posts: 26
Default

Quote:
Originally Posted by 2nelly View Post
By the way GRanges is a good approach
It's been by far the easiest approach I've found to SV annotation. My package isn't part of bioconductor yet as my linking between the two break-end for each breakpoint is just a $partner column and I suspect the BioConductor powers that be would want more S4 classes.

The real value in the package is in the GRanges conversion that works for most popular callers^, and findBreakpointOverlaps() for SV call matching.

^ I've tested breakdancer, cortex, crest, delly, gasv, gridss, hydra, lumpy, manta, pindel, socrates, tigra. It would be really nice if more callers adhered to the VCF specifications when they output VCF.
dcameron is offline   Reply With Quote
Reply

Tags
breakdancer help, delly

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:35 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO