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From: Kimberly O. <oln...@ic...> - 2015-04-17 18:49:47
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Hello,
I am a little confused on how to get some information that I would like o have.
What I would like to know is how many individuals have Allele 1(Ref) vs. Allele 2 (Alt) and if at all possible which individuals.
so Something like this:
Allele1 Allele2 Count1 Count2 MAF
A T 90 9 If possible I would like to know how many out of my 99 individuals have the minor allele 2/99?
I have 99 CEU individuals from the 1000geneome project and am looking at chromosome 13
what I have done so far is gotten allele frequency using and frequency count:
out.frq
CHROM POS N_ALLELES N_CHR {ALLELE:FREQ}
13 19020047 2 198 A:1 T:0
13 19020074 2 198 C:1 A:0
13 19020078 2 198 C:1 T:0
13 19020095 2 198 C:0.964646 T:0.0353535
13 19020116 2 198 C:0.994949 T:0.00505051
13 19020125 2 198 C:1 A:0
13 19020165 2 198 T:1 A:0
and
out.frq.count
CHROM POS N_ALLELES N_CHR {ALLELE:COUNT}
13 19020047 2 198 A:198 T:0
13 19020074 2 198 C:198 A:0
13 19020078 2 198 C:198 T:0
13 19020095 2 198 C:191 T:7
13 19020116 2 198 C:197 T:1
Is it possible to get the name/number of that individuals that have allele2? and the count of how many individuals have C vs T?
Thank you,
Kimberly
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