From 41d6a634919252f60c9e5fd6fe90fd5b68ca5c97 Mon Sep 17 00:00:00 2001 From: Zachary Szpiech Date: Fri, 22 Oct 2021 16:43:26 -0400 Subject: [PATCH] v2.0.0 --- README | 118 +++++++++++++-------------------------------------------- 1 file changed, 27 insertions(+), 91 deletions(-) diff --git a/README b/README index c32a25a..284fe49 100644 --- a/README +++ b/README @@ -11,6 +11,8 @@ thus reported as log(iHH1/iHH0) based on the coding you have provided. Citations: +ZA Szpiech (2021) selscan 2.0: scanning for sweeps in unphased data. biorxiv doi: + doi:10.1101/2021.10.22.465497. ZA Szpiech and RD Hernandez (2014) selscan: an efficient multi-threaded program to calculate EHH-based scans for positive selection. Molecular Biology and Evolution 31: 2824-2827. @@ -31,7 +33,9 @@ BF Voight et al. (2006) A map of recent positive selection in the human PC Sabeti et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832–837. - +22OCT2021 - selscan v2.0.0 - Introducing unphased versions of iHS, nSL, XP-EHH, and XP-nSL. Use with --unphased flag. See ZA Szpiech (2021) Biorxiv for details. Normalize as you would with the unphased + statistics. + 20MAY2020 - selscan v1.3.0 - Log ratios are now output as log10 not natural logs (beware comparisons with raw selscan computations from versions prior to v1.3.0). New statistics implemented. --pmap : Set this flag to use physical distance instead of genetic map @@ -169,7 +173,25 @@ Exactly one of these must be specified when running norm (e.g. ./norm --ihs --fi USAGE: -**Data must be phased and have no missing genotypes.** +**Data must have no missing genotypes.** + +selscan v2.0.0 -- a program to calculate EHH-based scans for positive selection in genomes. +Source code and binaries can be found at . + +selscan currently implements EHH, iHS, XP-EHH, and nSL. + +Citations: + +selscan: ZA Szpiech and RD Hernandez (2014) MBE 31: 2824-2827. + ZA Szpiech (2021) biorxiv: doi:10.1101/2021.10.22.465497. +iHH12: R Torres et al. (2018) PLoS Genetics 15: e1007898. + N Garud et al. (2015) PLoS Genetics 11: 1–32. +nSL: A Ferrer-Admetlla et al. (2014) MBE 31: 1275-1291. +XP-nSL: Szpiech et al. (2021) Evol Lett 5: 408-421. +XP-EHH: PC Sabeti et al. (2007) Nature 449: 913–918. + K Wagh et al. (2012) PloS ONE 7: e44751. +iHS: BF Voight et al. (2006) PLoS Biology 4: e72. +EHH: PC Sabeti et al. (2002) Nature 419: 832–837. To calculate EHH: @@ -299,6 +321,9 @@ in the construction of your haplotypes please use the --keep-low-freq flag. Normal function is to disregard the score for that core. Default: false +--unphased : Set this flag to use multilocus genotypes. + Default: false + --vcf : A VCF file containing haplotype data. A map file must be specified with --map. Default: __hapfile1 @@ -319,92 +344,3 @@ in the construction of your haplotypes please use the --keep-low-freq flag. --xpnsl : Set this flag to calculate XP-nSL. Default: false - - - -################################################################################ -################################################################################ - -norm v1.3.0 -- a program for downstream analysis of selscan output -Source code and binaries can be found at - - -Citations: - -selscan: ZA Szpiech and RD Hernandez (2014) MBE, 31: 2824-2827. -iHH12: R Torres, et al. (2017) bioRxiv, doi: https://doi.org/10.1101/181859. - N Garud, et al. (2015) PLoS Genetics, 11: 1–32. -nSL: A Ferrer-Admetlla, et al. (2014) MBE, 31: 1275-1291. -xpehh: PC Sabeti, et al. (2007) Nature, 449: 913–918. -iHS: BF Voight, et al. (2006) PLoS Biology, 4: e72. - -To normalize selscan output across frequency bins: - -./norm [--ihs|--xpehh|--nsl|--xpnsl|--ihh12] --files ... - -To normalize selscan output and analyze non-overlapping windows of fixed bp for -extreme scores: - -./norm [--ihs|--xpehh|--nsl|--xpnsl|--ihh12] --files ... --bp-win - -----------Command Line Arguments---------- - ---bins : The number of frequency bins in [0,1] for score normalization. - Default: 100 - ---bp-win : If set, will use windows of a constant bp size with varying - number of SNPs. - Default: false - ---crit-percent : Set the critical value such that a SNP with iHS in the most extreme CRIT_PERCENT tails (two-tailed) is marked as an extreme SNP. - Not used by default. - Default: -1.00 - ---crit-val : Set the critical value such that a SNP with |iHS| > CRIT_VAL is marked as an extreme SNP. Default as in Voight et al. - Default: 2.00 - ---files ... : A list of files delimited by whitespace for - joint normalization. - Expected format for iHS or nSL files (no header): - - Expected format for XP-EHH files (one line header): - - Expected format for iHH12 files (one line header): - - Default: infile - ---first : Output only the first file's normalization. - Default: false - ---help : Prints this help dialog. - Default: false - ---ihh12 : Do ihh12 normalization. - Default: false - ---ihs : Do iHS normalization. - Default: false - ---log : The log file name. - Default: logfile - ---min-snps : Only consider a bp window if it has at least this many SNPs. - Default: 10 - ---nsl : Do nSL normalization. - Default: false - ---qbins : Outlying windows are binned by number of sites within each - window. This is the number of quantile bins to use. - Default: 10 - ---winsize : The non-overlapping window size for calculating the percentage - of extreme SNPs. - Default: 100000 - ---xpehh : Do XP-EHH normalization. - Default: false - ---xpnsl : Do XP-nSL normalization. - Default: false -