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.
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.
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