which R package to use to do Quality control for SNPs data
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7.0 years ago
mms140130 ▴ 60

Hello,

I have a large SNP data, I'm trying to remove the SNPs with minor allele frequency (MAF) < 5% and the ones that don't follow Hardy-weinberg equilibrium . I'm using R and I don't know which package does that any help please

SNP R snp • 3.4k views
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7.0 years ago
willgilks ▴ 360

Hi MMS,

You could try https://cran.r-project.org/web/packages/vcfR/index.html although without meaning to sound intentionally vain, I think my graphs are better :) https://f1000research.com/articles/5-2644/v3 with code available at https://zenodo.org/record/159272#.WKCKsBAnp7E. To visualise the qc using R you can use GATK variantsToTable function to make a readable table. https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_VariantsToTable.php

GATK also has a Hard-Weinberg calculator but I'm not sure about filtering variants directly https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_annotator_HardyWeinberg.php

If you don't use GATK, then programs like vcfTools and bcfTools could probably help, otherwise you have you write your own Perl/Bash/Python/whatever scripts. Plink 1.9 is good too https://www.cog-genomics.org/plink2. You have to convert your vcf into just plink format genotypes, then it's easy to filter by MAF, and HWE.

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Thank you , I appreciate your help

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