Remove indels from VCF file- not working

Question

[gaurab.bhattarai46]

Hi,

I am trying to remove indels sites from vcf file. I used following command line;

vcftools --vcf inputfile.vcf --remove-indels --recode --recode-INFO-all --out outputfile

It still keeps all sites without removing indels. Please anybody has a solution for this? Thanks in advance.

[gaurab.bhattarai46]

Hi Kevin, Thank you so much for this information. I am kind of new to the bioinformatics. So, if you can suggest me the bcf command line to remove indels, it will help me a lot. In my SNPs data, there are both '-' indels as well as '0' i,e -/+ are present (Based on IUPAC). Thanks in advance.

[Pierre Lindenbaum]

, there are both '-' indels as well as '0' i,e -/+ are present (Based on IUPAC)

?

can you please show us such line please

Answer 1

[Kevin Blighe]

VCFtools is more or less deprecated, and even one of the co-authors of VCFtools (with whom I had the courtesy of having lunch one day) suggest to use BCFtools.

So, tis will do it for you:

bcftools view --types snps

Kevin