Question: Remove indels from VCF file- not working
0
gravatar for gaurab.bhattarai46
20 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 • 1.4k views
ADD COMMENTlink modified 20 months ago • written 20 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 20 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 20 months ago by Pierre Lindenbaum124k
0
gravatar for Kevin Blighe
20 months ago by
Kevin Blighe52k
Kevin Blighe52k 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 20 months ago by Kevin Blighe52k
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