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

[LauraSmith]

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]

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]

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]

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-Analysis/Tools/GFF-to-VCF-Python

[splaisan]

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