Remove snps with missing names

Question

[bha]

I pruned the 1000G data with MAF, and some LD filtering. I wonder there are some snps with names as "." (snps indentifiers are as "." dot). Any suggestion how i should remove or pull out that ones?

[cpad0112]

Use bcftools. There are two ways (copy/pasted from bcftools manual):

 "." to test missing values

Example:

 bcftools view -i 'ID=="."' test.vcf

.

    -n, --novel
        print novel sites only (ID column is ".")

Example :

    bcftools view -n test.vcf

[bha]

How i can remove these IDs (".") from the the datasets?

[cpad0112]

are these datasets in VCF format? if not, please post example dataset/records here.

[bha]

yes, these are in VCF format.

[Ram]

Like cpad0112 said, use bcftools. bcftools view can be used to subset data when the output is redirected to a file.

[cpad0112]

replace test. vcf with your dataset.vcf

example code:

 bcftools view -n kg.vcf > new.vcf