SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
VCF output from FreeBayes cigsit Bioinformatics 4 12-20-2012 12:44 AM
varscan output jgSoton Bioinformatics 1 12-20-2011 08:39 AM
Is VCF output mixing the MQ and Phred scores? AmitL Bioinformatics 6 09-29-2011 07:32 AM
SNP vcf output: GT vs PL shuang Bioinformatics 0 08-09-2011 02:08 PM
QC in GATK VCF output jorge Bioinformatics 2 07-26-2011 10:34 PM

Reply
 
Thread Tools
Old 02-07-2012, 02:20 AM   #1
OlgaMikh
Junior Member
 
Location: UK

Join Date: Feb 2012
Posts: 8
Default VarScan output to VCF

Hi all,
my question might seem simple but I'm new to NGS so please help me..!
I was working with VarScan programme, used "pileup2snp" option. The result is a txt file with a list of SNPs. Now I want to annotate them, i.e. figure out which ones are synonymous, present in dbSNP, 1000 genomes etc..
I have chosen Ensembl Effect Predictor to start with, but it wants the input file to be in vcf format or tab separated values.

How to convert my VarScan output into vcf?

Thanks in advance,
Olga.
OlgaMikh is offline   Reply With Quote
Old 02-07-2012, 02:28 AM   #2
Jane M
Senior Member
 
Location: Paris

Join Date: Aug 2011
Posts: 239
Default

I cannot help you with Ensembl Effect Predictor, but I can suggest you to start with Annovar, which is easy to use!
Jane M is offline   Reply With Quote
Old 02-07-2012, 04:06 AM   #3
OlgaMikh
Junior Member
 
Location: UK

Join Date: Feb 2012
Posts: 8
Default

Ok, thanks, Annovar really seems to be powerful.
As I understood i need to additionaly download hg19 snp132 file for annotation of hg19 data?
OlgaMikh is offline   Reply With Quote
Old 02-07-2012, 05:00 AM   #4
Jane M
Senior Member
 
Location: Paris

Join Date: Aug 2011
Posts: 239
Default

What is this file? A file containing the known snp, as in dbsnp?
I do not have downloaded such a file. Everything you need to download will be specified by annovar if missing.
Besides that, you only have to provide the file containing your list of snps or insertions/deletions:
Quote:
chr1 ref variant position_start_of_mutation position_end_of_mutation
Jane M is offline   Reply With Quote
Old 06-07-2012, 11:46 PM   #5
oliviajm
Member
 
Location: france

Join Date: Apr 2012
Posts: 13
Default

Quote:
Originally Posted by OlgaMikh View Post
Hi all,
my question might seem simple but I'm new to NGS so please help me..!
I was working with VarScan programme, used "pileup2snp" option. The result is a txt file with a list of SNPs. Now I want to annotate them, i.e. figure out which ones are synonymous, present in dbSNP, 1000 genomes etc..
I have chosen Ensembl Effect Predictor to start with, but it wants the input file to be in vcf format or tab separated values.

How to convert my VarScan output into vcf?

Thanks in advance,
Olga.
Hi Olga,

if you're still interested in using a vcf file, I've seen that the latest version of VarScan can output a vcf file with the otpion --output-vcf.

Olivia
oliviajm is offline   Reply With Quote
Reply

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 08:33 AM.


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