VarScan output to VCF

[OlgaMikh]

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.

[Jane M]

I cannot help you with Ensembl Effect Predictor, but I can suggest you to start with Annovar, which is easy to use!

[OlgaMikh]

Ok, thanks, Annovar really seems to be powerful.
As I understood i need to additionaly download hg19 snp132 file for annotation of hg19 data?

[Jane M]

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:

chr1 ref variant position_start_of_mutation position_end_of_mutation

[oliviajm]

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