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I have a set of SNPs (single nucleotide polymorphisms) { S1, S2, ..., SN } from approximately 200 humans. I wish to determine the linkage disequilibrium (LD) for a defined subset of these SNPs. By this I mean e.g. I would like to compute e.g. LD between S1 and S2, S3, S4, but not the LD between S2 and S3.
Could this calculation be performed in PLINK?
Yes, you can do this with plink.
You can use the flag --ld-snp <variant_id> to calculate LD between your SNP of interest and all other SNPs.
If you have multiple SNPs of interest, and want each of those compared with every SNP in your dataset, use --ld-snps <snp1-snp100,snp102,snp104>
A final option to calculate LD between a specific pair of SNPs is --ld <variant_id1> <variant_id2>
Anyway, it would be fairly easy via the filtering options here
The --exclude-snp is what you are wanting.
I have worked in LD and subsampling a genome is open to forcing a result. The alternative approach is the subsample is the population, or examine disequilibrium with respect to the physical chromosome. A local shift in disequilibrium or heterozygosity (sliding window along a chromosome) is an indication of selective pressure. This approach is frequently used in eukaryotic parasites to identify drug resistance. I don't have experience of human genetics but there are certainly enough here who do. However, I think you need to define the biological rationale for the subsample. Just having loads of data is easily resolved because any algorithm can be written to handle automation.
