Question: Need some help regarding format compatible with VEP online tools
gravatar for ivivek_ngs
5.7 years ago by
Seattle,WA, USA
ivivek_ngs4.9k wrote:

Dear All,

I have some INDELS which I have found out using the VarScan2. However I did not use the vcf output and also the am only caring about somatic indels. So I filter the indel output of VarScan2 and just retain the somatic indels in a .txt file in the below format. 

chr1 976506 A -GCGGGGGC
chr1 1141864 C +G
chr1 1417649 T -C
chr1 1454046 T -AC
chr1 2117710 A -C
chr1 2494360 C -T
chr1 2985791 A +G

I now want to annotate this using VEP. I have already annotated with Annovar and it works fine but it does not work with the VEP tool at ENSEMBL website as the format is not compatible. I also created a script to convert .txt file to vcf4 format which worked well with annovar for the same .txt indels which I converted to vcf4 format with my script. But this vcf files are not being recognized by ENSEMBL website. So my only way is to make this format somewhere compatible with VEP online. Can anyone suggest me a script or way how to do it? Or does anyone have any other script to tranform .txt to VCF4 that is compatible with ENSEMBL VEP tool in their webpage? I would appreciate some leads in this front.

sequencing snp next-gen • 2.5k views
ADD COMMENTlink modified 5.7 years ago by Emily_Ensembl21k • written 5.7 years ago by ivivek_ngs4.9k
gravatar for Ashutosh Pandey
5.7 years ago by
Ashutosh Pandey12k wrote:

VEP accepts these formats

The first format is pretty close to what you have. Modify little more and you should be good to go. 

ADD COMMENTlink written 5.7 years ago by Ashutosh Pandey12k

Yes I know the format that VEP accepts, I would need some help if anyone has any script that can modify this format to VEP format, if its possible. Infact I have to create the start end for all and then ref and alt as well. to get the desired VEP format which is the default one.

ADD REPLYlink written 5.7 years ago by ivivek_ngs4.9k

@ Ashutosh Pandey is there any way I can make the indel out of VarScan2 into VEP format ? Any suggestions?

ADD REPLYlink written 5.7 years ago by ivivek_ngs4.9k

VEP accepts pileup, hgvs notations, variant identifiers (e.g. rs), vcf, and what we call Ensembl default (1 234 234 G/T). We are having problems with the online version now but the team is working on fixing the problem asap. See more details on my reply at C: Annotating variants with Annovar, Oncotator and SnpEFF

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by Denise - Open Targets5.1k

It is working now , I have got the results

ADD REPLYlink written 5.7 years ago by ivivek_ngs4.9k
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