Description Usage Arguments Author(s)
Function to compute linkage disequilibrium (LD) from phased data. The LD is computed between a SNP of interest and all other SNPs within a specified window around it.
1 |
phase_file |
The name of the input file with phased genotypes in the VCF format. |
snps_file |
The name of the input file with the list of SNP identifiers (one per line). The SNP identifier can be an rsID, chromosomal position in base-pairs or any other identifier format that is present in phase_file. For every SNP in the list, the LD between it and all other SNPs within a specified window around it is computed. |
output_file |
The name of the output file. Output file includes five tab-separated columns. The first four columns are: FIRST_MARKER, FIRST_BP, SECOND_MARKER, SECOND_BP. The last column depends on the specified coefficient and can be D, DPRIME or R2, accordingly. |
window |
The number of base pairs to consider around every SNP of interest. |
coefficient |
The LD coefficient to be calculated between a pair of SNPs. The supported LD coefficients are "d" (D), "dprime" (D') or "r2" (r^2). |
maf |
Minor Allele Frequency (MAF) threshold: SNPs with MAF <= maf will not be considered. The threshold may vary from 0 (default) to 0.5. |
gzip |
TRUE if output file is in gzip format. |
Daniel Taliun, Johann Gamper, Cristian Pattaro
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.