SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to transform BAM format to .TXT or .BED? zhenshao Bioinformatics 12 11-14-2015 05:03 PM
Updated How to convert .txt file to .bed .GFF or .BAR file format, forevermark4 Bioinformatics 2 06-30-2014 05:02 AM
How to convert .txt file to .bed or .gff, How can we use chip seq data in R software forevermark4 Bioinformatics 57 06-30-2014 05:01 AM
Converter for vcf to bed format ketan_bnf Bioinformatics 4 09-03-2013 04:43 AM
need help with converting VCF to GTF/GFF format rudi283 Bioinformatics 4 03-05-2011 10:49 AM

Reply
 
Thread Tools
Old 12-05-2011, 08:51 AM   #1
LauraSmith
Junior Member
 
Location: SAN FRANCISCO

Join Date: Dec 2011
Posts: 4
Post Is there a tool that converts TXT, BED, GFF format to VCF?

Hi,

I would like to ask if there is tool out there that would convert variants in a certain file format (such as .txt, .gff, .bed) to VCF format?

Thank you for your help.
Laura
LauraSmith is offline   Reply With Quote
Old 12-05-2011, 09:14 AM   #2
mbblack
Senior Member
 
Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245
Default

PacBio's SMRT suite has a python script to supposedly go from GFFv4 to VCF.

But, I recall on the BEDTools discussion board, Aaron Quinlan has mentioned that going from GFF or BED to VCF is not a simple task, unless the input files were originally created to track all the information required for the VCF output. That makes it difficult to write generic scripts for conversion.
mbblack is offline   Reply With Quote
Old 12-05-2011, 11:30 AM   #3
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

Quote:
Originally Posted by mbblack View Post
PacBio's SMRT suite has a python script to supposedly go from GFFv4 to VCF.
Was that a typo? Did you mean GFF v3 perhaps?
maubp is offline   Reply With Quote
Old 12-05-2011, 11:32 AM   #4
mbblack
Senior Member
 
Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245
Default

Quote:
Originally Posted by maubp View Post
Was that a typo? Did you mean GFF v3 perhaps?
I was just glancing at their website, but I think it means their script is v.4 (or the entire SMRT suite is v.4), not that they've created their own GFF version!

http://www.pacbiodevnet.com/SMRT-Ana...-to-VCF-Python

Last edited by mbblack; 12-05-2011 at 11:35 AM.
mbblack is offline   Reply With Quote
Old 03-22-2017, 01:41 AM   #5
splaisan
senior molecular biologist
 
Location: Belgium

Join Date: Jun 2009
Posts: 31
Default

In my hands, the VCF v3.3 (exotic version if one with weird call syntax for the ALT field) format produced by SMRTv4 accompanying gffToVcf (v3.0 - pbgenomicconsensus) is not conform to the VCF4 specs and when used with VCF compatible tools, leads to errors.

Here an example from a very simple run
<pre>
##fileformat=VCFv3.3
##fileDate=2017121
##source=gffToVcf --resolved-tool-contract /opt/pacbio/userdata/jobs_root/000/000096/tasks/genomic_consensus.tasks.gff2vcf-0/resolved-tool-contract.json
##INFO=NS,1,Integer,"Number of Samples with Data"
##INFO=DP,1,Integer,"Total Depth of Coverage"
#CHROM POS ID REF ALT QUAL FILTER INFO
chromosome_2 486515 . C T 93.00 0 NS=1;DP=47
chromosome_2 487451 . C D1 93.00 0 NS=1;DP=47
chromosome_2 511331 . . IA 41.00 0 NS=1;DP=52
chromosome_2 537571 . . IA 55.00 0 NS=1;DP=40
chromosome_2 636693 . A G 93.00 0 NS=1;DP=31
chromosome_2 643391 . G T 93.00 0 NS=1;DP=46
chromosome_2 643959 . A D1 93.00 0 NS=1;DP=50
</pre>

Before I adventure in this, does anyone have a GFF3 to VCF4 converter that works on Sequel data?
Fields required to make a VCF from their GFF3 are there, it is 'only' a matter of operating a smart conversion between the two tabular formats and fixing coordinate issues and alternate allele cases (if present?!).
Thanks
splaisan is offline   Reply With Quote
Reply

Tags
bed, gff, vcf format

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 01:11 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO