Minor allele count report with --freq count in PLINK2
1
1
Entering edit mode
3.7 years ago
L_to_the_m ▴ 10

Hi, I have a dataset of 451 diploid humans in PLINK2. When trying to get the count report of the minor alleles in PLINK2 with this code:

plink2 --pfile file --freq counts

I will get a table like this:

CHROM   ID  REF ALT ALT_CTS OBS_CT
1   AX-13191280__rs3131972  G   A   169 902
1   AX-32225497__rs3131962  G   A   139 900
1   AX-11214939__rs12562034 G   A   84  902
1   AX-32355233__rs12131377 C   G   59  894
1   AX-32359895__rs61768212 G   C   452 898
1   AX-32365087__rs11240779 A   G   222 900
1   AX-32366075__rs57181708 A   G   90  898
1   AX-40293871__rs4970383  C   A   222 898
1   AX-32432755__rs4970382  T   C   352 900
1   AX-40308003__rs950122   G   C   183 902
1   AX-32459995__rs13303222 G   A   136 900
1   AX-32461903__rs6657440  T   C   330 902
1   AX-32488633__rs4970459  C   T   192 902
1   AX-32519659__rs74047407 G   A   209 900
1   AX-40357457__rs1110052  T   G   249 902
1   AX-32571027__rs2272757  A   G   306 900
1   AX-32572119__rs35471880 G   A   67  894
1   AX-32598061__rs13303065 T   C   307 900
1   AX-40388697__rs13303010 A   G   86  900

But sometimes I get a Alternate allele count which is for example ALT_CTS= 452 (as in line 5). How can this be since I only have 451 diploid individuals? Is it then then still the minor allele?

PLINK MAF • 2.4k views
ADD COMMENT
0
Entering edit mode

Couldn't one sample have more than one alteration?

ADD REPLY
0
Entering edit mode

This makes sense, and then the number is the sum of all minor alleles? And in total this result in a bigger number?

ADD REPLY
0
Entering edit mode

That is what I would assume. I would definitely look into it closer. I've had a similar problem before but the issue was more clear where ALT looked more like C,A instead of just C

ADD REPLY
3
Entering edit mode
3.7 years ago

ALT alleles are not guaranteed to be minor.

ADD COMMENT
0
Entering edit mode

Ok, is there a way to only get the minor alleles?

ADD REPLY
1
Entering edit mode

You can use --maj-ref force --make-pgen to swap all major alleles to REF, and then run --freq counts on the resulting output.

ADD REPLY

Login before adding your answer.

Traffic: 1381 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6