From ecee582ecf92afea91b4c30cde27df47b6b57625 Mon Sep 17 00:00:00 2001 From: "Filipe G. Vieira" Date: Fri, 2 Sep 2022 09:52:58 +0200 Subject: [PATCH] Updated help descriptions --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 1a6c108..00759ce 100644 --- a/README.md +++ b/README.md @@ -55,10 +55,10 @@ Executables are built into the main directory. If you wish to clean all binaries * `--max_kb_dist DOUBLE`: maximum distance between SNPs (in Kb) to calculate LD. Set to `0`(zero) to disable filter. [100] * `--max_snp_dist INT`: maximum distance between SNPs (in number of SNPs) to calculate LD. Set to `0` (zero) to disable filter. [0] * `--min_maf DOUBLE`: minimum SNP minor allele frequency. [0.001] -* `--ignore_miss_data`: ignore missing genotype data from analyses. +* `--ignore_miss_data`: ignore missing genotype data from analyses (e.g. MAF and haplotype frequency estimation). * `--call_geno`: call genotypes before running analyses. -* `--N_thresh DOUBLE`: minimum threshold to consider site; missing data if otherwise (assumes -call_geno). -* `--call_thresh DOUBLE`: minimum threshold to call genotype; left as is if otherwise (assumes -call_geno). +* `--N_thresh DOUBLE`: minimum threshold to consider position; if highest GL is lower, set as missing data (assumes -call_geno). +* `--call_thresh DOUBLE`: minimum threshold to call genotype; if highest GL is lower, left as is (assumes -call_geno). * `--rnd_sample DOUBLE`: proportion of comparisons to randomly sample. [1] * `--seed INT`: random number generator seed for random sampling (--rnd_sample). * `--extend_out`: print extended output (see below).