I am trying to filter a BED file that was downloaded. I am trying to filter it with plink but to no avail. I can get the commands to 'work' but the program is not filtering any samples as the output is the same as the input. I have also
This is what I am trying to do:
--bfile SouthernArc_Public --keep sampleids.txt --make-bed --allow-no-sex --out filtered PLINK v1.90b6.21 64-bit (19 Oct 2020) www.cog-genomics.org/plink/1.9/ (C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to filtered.log. Options in effect: --allow-no-sex --bfile SouthernArc_Public --keep sampleids.txt --make-bed --out filtered
32011 MB RAM detected; reserving 16005 MB for main workspace. 1233013 variants loaded from .bim file. 5940 people (3341 males, 2505 females, 94 ambiguous) loaded from .fam. Ambiguous sex IDs written to filtered.nosex . 5940 phenotype values loaded from .fam. Error: No people remaining after --keep.
I know that the sample names are correct as I did a grep on the SouthernArc_Public.fam file to make sure my sample names match. For instance, here is my input file for the --keep command: head sampleids.txt I15705 I15705 I13838 I13838 I13840 I13840 I14689 I14689 I8471 I8471 I14691 I14691 I17622 I17622 I14690 I14690 I14692 I14692 I16251 I16251
I know that I15705 is in the ped file. Thus, I am not sure why it is saying no people are remaining.
Any help would greatly be appreciated!