Closed josieparis closed 5 years ago
Hi Josie,
Yes, if the second allele is the derived allele, then $8*$4 is correct. Good catch! I've updated the FAQ page with the revised command, and added mention of the --derived flag so that the derived allele will be listed second when people use vcftools.
Thank you! Katie
No worries! Thanks!
Hey Katie!
Am using your awk code (you emailed me before) for generating the input files from the vcfs and think there's a typo:
awk -F "\t|:" '(NR>1) && ($6!='0') && ($6!='1') && ($3=='2') {OFS="\t"; print$2,$6*$4,$4}' chr1.AA.APHP.out.frq
should be:
awk -F "\t|:" '(NR>1) && ($6!='0') && ($6!='1') && ($3=='2') {OFS="\t"; print$2,$8*$4,$4}' chr1.AA.APHP.out.frq
just to demonstrate: the vcf line looks like this: chr1 4827 chr1_4827 G A 38420.2 PASS AA=G
the vcftools freqs line looks like this: chr1 4827 2 24 G 0.416667 A 0.583333
so A is the derived allele, and therefore the code should be column 8* sample size?
4827 14 24
not 4827 10 24
thanks! josie