I want to filter variants according to MAF < 0.001 but I dont know which programs will I have to use ?
I used plink: ./plink --vcf myfile.vcf --maf 0.001--recode vcf --out myfilefiltered.vcf
Thanks!! I'll try :)
plink-1.07-x86_64 v1.07 version
It works :)
I got some errors as ;
Unused command line option: vcf
Unused command line option: --vcf
Writing this text to log file [ myfilefiltered.vcf.log ]
Could you please help me and is it working for vcf file ?
PLINK is only usable here if you only need to keep hard genotype calls from the VCF. Otherwise, you should use vcftools (http://vcftools.sourceforge.net/ ) or a similar VCF-based program.
The value in the GT field. PLINK will only track whether the genotype call is 0/0, 0/1, 1/1, or missing; if there is any other information in the VCF (e.g. genotype likelihoods, read depths) it is ignored by PLINK.
Also, if there is more than one ALT allele, PLINK currently throws out all but the most common one; this will be fixed, but it will take a fairly long time.
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