Is there a tool that converts TXT, BED, GFF format to VCF?

LauraSmith · 12-05-2011, 09:51 AM

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

mbblack · 12-05-2011, 10:14 AM

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.

maubp · 12-05-2011, 12:30 PM

Quote:

Originally Posted by mbblack

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?

mbblack · 12-05-2011, 12:32 PM

Quote:

Originally Posted by maubp

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

splaisan · 03-22-2017, 02:41 AM

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

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

12-05-2011, 09:51 AM	#1
LauraSmith Junior Member Location: SAN FRANCISCO Join Date: Dec 2011 Posts: 4	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

03-22-2017, 02:41 AM	#5
splaisan senior molecular biologist Location: Belgium Join Date: Jun 2009 Posts: 31	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 __________________ http://www.bits.vib.be/index.php

12-05-2011, 10:14 AM	#2
mbblack Senior Member Location: Research Triangle Park, NC Join Date: Aug 2009 Posts: 245	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.