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Minor Allele Frequency Filtration
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4.1 years ago
basalganglia • 30
England

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

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14 months ago
fusion.slope • 200

I used plink: ./plink --vcf myfile.vcf --maf 0.001--recode vcf --out myfilefiltered.vcf

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Thanks!! I'll try :)

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<html><head></head><body style="background-color: rgb(255, 255, 255); line-height: initial;"> Which plink version are you using? Invio eseguito dallo smartphone BlackBerry 10. **Da:** basalganglia on Biostar **Inviato:** domenica 29 marzo 2015 21:21 **A:** andreani.tommaso86@gmail.com **Rispondi a:** biostar+f25f9908+code@biostars.io **Oggetto:** [biostar] Minor Allele Frequency Filtration --- Activity on a post you are following on [Biostar](http://www.biostars.org) User [basalganglia](http://www.biostars.org/u/15418/) wrote [C: Minor Allele Frequency Filtration](http://www.biostars.org/p/136256/#136327): Thanks!! I'll try :) * * * You may reply via email or visit [C: Minor Allele Frequency Filtration](http://www.biostars.org/p/136256/#136327) </body></html>
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plink-1.07-x86_64 v1.07 version

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<html><head></head><body style="background-color: rgb(255, 255, 255); line-height: initial;"> 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/> Invio eseguito dallo smartphone BlackBerry 10. **Da:** basalganglia on Biostar **Inviato:** domenica 29 marzo 2015 23:26 **A:** andreani.tommaso86@gmail.com **Rispondi a:** biostar+32b70a6b+code@biostars.io **Oggetto:** [biostar] Minor Allele Frequency Filtration --- Activity on a post you are following on [Biostar](http://www.biostars.org) User [basalganglia](http://www.biostars.org/u/15418/) wrote [C: Minor Allele Frequency Filtration](http://www.biostars.org/p/136256/#136343): plink-1.07-x86_64 * * * You may reply via email or visit [C: Minor Allele Frequency Filtration](http://www.biostars.org/p/136256/#136343) </body></html>
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It works :)

thanks !!

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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 !!!

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16 months ago
United States

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.

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Could you please explain what does it mean "hard Genotype calls"? Thanks! P.s. I have worked with 39 vcf files
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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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<html><head></head><body style="background-color: rgb(255, 255, 255); line-height: initial;"> Ah ok thank you very much for this information!! Invio eseguito dallo smartphone BlackBerry 10. **Da:** chrchang523 on Biostar **Inviato:** domenica 29 marzo 2015 22:03 **A:** andreani.tommaso86@gmail.com **Rispondi a:** biostar+3c90de3e+code@biostars.io **Oggetto:** [biostar] Minor Allele Frequency Filtration --- Activity on a post you are following on [Biostar](http://www.biostars.org) User [chrchang523](http://www.biostars.org/u/9575/) wrote [C: Minor Allele Frequency Filtration](http://www.biostars.org/p/136256/#136334): 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. * * * You may reply via email or visit [C: Minor Allele Frequency Filtration](http://www.biostars.org/p/136256/#136334) </body></html>
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