Question: Remove indels from VCF file- not working
0
gravatar for gaurab.bhattarai46
14 months ago by
gaurab.bhattarai460 wrote:

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.

snp software error • 833 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by gaurab.bhattarai460

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.

ADD REPLYlink written 14 months ago by gaurab.bhattarai460

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

?

can you please show us such line please

ADD REPLYlink written 14 months ago by Pierre Lindenbaum120k
0
gravatar for Kevin Blighe
14 months ago by
Kevin Blighe43k
Republic of Ireland
Kevin Blighe43k wrote:

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

ADD COMMENTlink written 14 months ago by Kevin Blighe43k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 850 users visited in the last hour