Hi there,
Could anyone show me a straightforward method to retrieve genotypic frequencies from a tped or vcf?
I mean, not the expected frequencies calculated assuming Hardy Weinberg equilibrium from the allelic frequencies, but the real genotypic frequencies.
I found a way using plink's --hardy option, which gives you the genotype counts, amongst many other stuff, and from these counts retrieve the frequencies. But I was wondering if a more simple way, analog the --freq option from plink or vcftools for the allelic frequencies. I know this may be a silly question, but had not found anything.
Thanks in advance,
P.
2 answers
Following one-liner will convert Plink --hwe output from counts to frequencies:
#remove header, substitute "/" to "tabs", calculate frequencies, output to new file
sed 1d myfile.hwe | \
sed 's:/:\t:g' | \
awk '{OFS="\t";print $1,$2,$3,$4,$5,($6/($6+$7+$8))"/"($7/($6+$7+$8))"/"($8/($6+$7+$8)),$9,$10,$11}' \
> myfile.hwe.freq
Example:
#input
CHR SNP TEST A1 A2 GENO O(HET) E(HET) P
22 rs2027653 ALL C T 489/1585/1498 0.4437 0.4601 0.0349
22 rs2027653 AFF C T 241/772/752 0.4374 0.4581 0.06132
22 rs2027653 UNAFF C T 248/813/746 0.4499 0.462 0.263
#output
22 rs2027653 ALL C T 0.136898/0.443729/0.419373 0.4437 0.4601 0.0349
22 rs2027653 AFF C T 0.136544/0.437394/0.426062 0.4374 0.4581 0.06132
22 rs2027653 UNAFF C T 0.137244/0.449917/0.412839 0.4499 0.462 0.263
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I don't understand the problem, please clarify. As
--freqwith--countswould give you counts? Also, try--modeloption, it gives all sorts of counts, too.I think it is clear enough... It is simply (to) "retrieve genotypic frequencies from a tped or vcf". Not genotype counts, but frequency numbers directly. I was just wondering if there was a method to retrieve it in the same format as when you retrieve the allele frequencies with vcftools or plink. That's all...