Problems removing a subset of individuals from ped files
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2.3 years ago
Nuthatch • 0

Hello everyone, I have a mydata.ped file, made up of 10215 rows (individuals) that looks like this:

1  MAL-005  0 0  1 1  3 3  4 4
2  MAL-006  0 0  3 3  1 1  4 4
3  MAL-007  1 1  0 0  1 3  4 4
4  MAL-008  1 1  0 1  1 3  3 4


Now I want to obtain a new ped file in which 3723 of the 10215 individuals in the original ped file have been removed. Just for the sake of giving you an example, let's say that I want to remove individuals 1 and 3. I've tried with this plink command on bash:

plink --file mydata --remove indtoremove.txt --out mydata_new --noweb


The indtoremove.txt is made up of two columns that look like this:

1  MAL-005
3  MAL-007


Plink seems to work, and after launching the command, these messages appear in the terminal:

Skipping web check... [ --noweb ]
Writing this text to log file [ mydata_new.log ]
Analysis started: Sun Aug 16 13:55:32 2020

Options in effect:
--file mydata
--remove indtoremove.txt
--out mydata_new
--noweb

597573 (of 597573) markers to be included from [ mydata.map ]
Warning, found 128 individuals with ambiguous sex codes
These individuals will be set to missing ( or use --allow-no-sex )
Writing list of these individuals to [ mydata_new.nosex ]
10215 individuals read from [ mydata.ped ]
10087 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 10087 controls and 128 missing
6169 males, 3918 females, and 128 of unspecified sex
3723 individuals removed with --remove option
Before frequency and genotyping pruning, there are 597573 SNPs
6492 founders and 0 non-founders found
Total genotyping rate in remaining individuals is 0.984567
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 597573 SNPs
After filtering, 0 cases, 6428 controls and 64 missing
After filtering, 4076 males, 2352 females, and 64 of unspecified sex

Analysis finished: Sun Aug 16 14:32:41 2020


Once analysis is finished, I don't get any new files, except for mydata_new.log and mydata_new.nosex. Can anyone tell me what's the problem? I thought I should get an output.ped, .map and .pedind file. Sorry if I'm missing something, but I'm new at bioinformatics. Is it possible that it's an issue of available space on the computer? Thank you.

plink remove ped • 547 views
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you have to add --recode to your command