Minor Allele Frequency Filtration

Question

[basalganglia]

Hi everybody,

I want to filter variants according to MAF < 0.001 but I dont know which programs will I have to use ?

Thanks,

BG

Answer 1

[fusion.slope]

I used plink:

./plink --vcf myfile.vcf --maf 0.001--recode vcf --out myfilefiltered.vcf

[basalganglia]

Thanks!! I'll try :)

[fusion.slope]

Which plink version are you using?

[basalganglia]

plink-1.07-x86_64 v1.07 version

[fusion.slope]

You should use plink 1.9, is the most updated and I worked using that version. See the link https://www.cog-genomics.org/plink2/

[basalganglia]

It works :)

Thanks!

[basalganglia]

Hi,

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 ?

Thanks !!!

Answer 2

[chrchang523]

PLINK is only usable here if you only need to keep hard genotype calls from the VCF. Otherwise, you should use vcftools or a similar VCF-based program.

[fusion.slope]

Could you please explain what does it mean "hard Genotype calls"? Thanks! P.s. I have worked with 39 vcf files

[chrchang523]

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.

[fusion.slope]

Ah ok thank you very much for this information!!