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v2.0.0
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szpiech committed Oct 22, 2021
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Expand Up @@ -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.
Expand All @@ -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 <bool>: Set this flag to use physical distance instead of genetic map
Expand Down Expand Up @@ -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 <https://www.github.com/szpiech/selscan>.

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:

Expand Down Expand Up @@ -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 <bool>: Set this flag to use multilocus genotypes.
Default: false

--vcf <string>: A VCF file containing haplotype data.
A map file must be specified with --map.
Default: __hapfile1
Expand All @@ -319,92 +344,3 @@ in the construction of your haplotypes please use the --keep-low-freq flag.
--xpnsl <bool>: 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
<https://www.github.com/szpiech/selscan>

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 <file1.*.out> ... <fileN.*.out>

To normalize selscan output and analyze non-overlapping windows of fixed bp for
extreme scores:

./norm [--ihs|--xpehh|--nsl|--xpnsl|--ihh12] --files <file1.*.out> ... <fileN.*.out> --bp-win

----------Command Line Arguments----------

--bins <int>: The number of frequency bins in [0,1] for score normalization.
Default: 100

--bp-win <bool>: If set, will use windows of a constant bp size with varying
number of SNPs.
Default: false

--crit-percent <double>: 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 <double>: 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 <string1> ... <stringN>: A list of files delimited by whitespace for
joint normalization.
Expected format for iHS or nSL files (no header):
<locus name> <physical pos> <freq> <ihh1/sL1> <ihh2/sL2> <ihs/nsl>
Expected format for XP-EHH files (one line header):
<locus name> <physical pos> <genetic pos> <freq1> <ihh1> <freq2> <ihh2> <xpehh>
Expected format for iHH12 files (one line header):
<locus name> <physical pos> <freq1> <ihh12>
Default: infile

--first <bool>: Output only the first file's normalization.
Default: false

--help <bool>: Prints this help dialog.
Default: false

--ihh12 <bool>: Do ihh12 normalization.
Default: false

--ihs <bool>: Do iHS normalization.
Default: false

--log <string>: The log file name.
Default: logfile

--min-snps <int>: Only consider a bp window if it has at least this many SNPs.
Default: 10

--nsl <bool>: Do nSL normalization.
Default: false

--qbins <int>: Outlying windows are binned by number of sites within each
window. This is the number of quantile bins to use.
Default: 10

--winsize <int>: The non-overlapping window size for calculating the percentage
of extreme SNPs.
Default: 100000

--xpehh <bool>: Do XP-EHH normalization.
Default: false

--xpnsl <bool>: Do XP-nSL normalization.
Default: false

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