ngs_server 0.1 → 0.2

data/ext/vcftools/website/src/options.inc

@@ -0,0 +1,654 @@
+
+<div class="item">
+<h1>vcftools: Usage and Options</h1>
+<p>The vcftools program is intended for analysis of <b>diploid SNP data</b> in VCF format. 
+The program is run from the command line, and the interface is
+inspired by <a href="http://pngu.mgh.harvard.edu/%7Epurcell/plink/">PLINK</a>,
+and so should be largely familiar to users of that package. Commands
+take the
+following form:</p>
+<p class="codebox">vcftools --vcf file1.vcf --chr 20 --freq
+</p>
+<p>The above command tells vcftools to read in the file <i>file1.vcf</i>, extract
+sites on chromosome 20, and calculate the allele frequency at each
+site. The resulting allele frequency estimates
+are stored in the output file, <i>out.freq</i>. As in the
+above example, output from vcftools is mainly sent
+to output files, as opposed to being shown on the screen.
+</p>
+<p>A description of each of the avaliable options follows. <b>Note that some commands may only be 
+available in the latest version of vcftools. To obtain the latest version, you should use SVN to 
+checkout the latest code, as described on the <a href="http://vcftools.sourceforge.net/index.html">home page</a>.</b>
+<br>
+<br>
+<br>
+<a href="#basic">Basic&nbsp;Options</a><br>
+<a href="#site_filter">Site Filter Options</a><br>
+<a href="#indv_filter">Individual Filters</a><br>
+<a href="#geno_filter">Genotype Filters</a><br>
+<a href="#stats">Output Statistics</a><br>
+<a href="#other_format">Output in Other Formats</a><br>
+<a href="#misc">Miscellaneous</a><br>
+<a href="#diff">File Comparison</a><br>
+<a href="#development">Options still in development</a><br>
+</p>
+</div>
+<div class="item">
+<h1><a name="basic" class="Q">Basic&nbsp;Options</a></h1>
+<ul>
+<li>--vcf &lt;filename&gt;</li>
+<br>
+This option defines the VCF file to be processed. The files need to be decompressed prior to use with vcftools. 
+<b>vcftools expects files in VCF format v4.0, a specification of which can be found <a href="specs.html">here</a></b>.  
+<br>
+<br>
+</li>
+<li>--gzvcf &lt;filename&gt;</li>
+<br>
+This option can be used in place of the --vcf option to read compressed (gzipped) VCF files directly. Note that this 
+option can be quite slow when used with large files.  
+<br>
+<br>
+</li>
+<li>--out &lt;prefix&gt;<br>
+<br>
+This option defines the output filename prefix for all files generated
+by vcftools. For example, if &lt;prefix&gt; is set to&nbsp;<span style="font-style: italic;">output_filename</span>,
+then all output files will be of the form <span style="font-style: italic;">output_filename.*** </span>.
+If this option is omitted, all output files will have the prefix 'out.'.<br>
+<br>
+</li>
+</ul>
+</div>
+<div class="item">
+<h1><a name="site_filter" class="Q">Site Filter Options</a></h1>
+<ul>
+<li>--chr &lt;chromosome&gt;<br>
+<br>
+Only process sites with a chromosome identifier matching
+&lt;chromosome&gt;<br>
+</li>
+<li>--from-bp &lt;integer&gt;</li>
+<li>--to-bp &lt;integer&gt;<br>
+<br>
+These options define the&nbsp;physical range of sites will be
+processed. Sites outside of this range will be excluded. These options
+can only be used in conjuction with --chr.<br>
+<br>
+</li>
+<li>--snp &lt;string&gt;<br>
+<br>
+Include SNP(s) with matching ID (e.g. a dbSNP rsID). This command can be used multiple
+times in order to include more than one SNP.<br>
+<br>
+</li>
+<li>--snps &lt;filename&gt;<br>
+<br>
+Include a list of SNPs given in a file. The file should contain a list
+of SNP IDs (e.g. dbSNP rsIDs), with one ID per line.<br>
+<br>
+</li>
+<li>--exclude &lt;filename&gt;<br>
+<br>
+Exclude a list of SNPs given in a file. The file should contain a list
+of SNP IDs, with one ID per line.<br>
+<br>
+</li>
+<li>--positions &lt;filename&gt;<br>
+<br>
+Include a set of sites on the basis of a 
+list of positions. Each line of the input file should contain a (tab-separated) chromosome and position.
+The file should have a header line. Sites not included in the list are excluded.<br>
+<br>
+</li>
+<li>--bed &lt;filename&gt;<br>
+<li>--exclude-bed &lt;filename&gt;<br>
+<br>
+Include or exclude a set of sites on the basis of a 
+<a href="http://genome.ucsc.edu/FAQ/FAQformat#format1">BED</a> file. Only 
+the first three columns (chrom, chromStart and chromEnd) are required. 
+The BED file should have a header line. <br>
+<br>
+</li>
+<li>--remove-filtered-all</li>
+<li>--remove-filtered &lt;string&gt;<br>
+<li>--keep-filtered &lt;string&gt;<br>
+<br>
+These options are used to filter sites on the basis of their FILTER flag. 
+The first option removes all sites with a FILTER flag. 
+The second option can be used to exclude sites with a specific filter flag. 
+The third option can be used to select sites on the basis of specific filter flags. The second and third options can be used multiple times to specify multiple FILTERs. 
+The --keep-filtered option is applied before the --remove-filtered option.<br>
+<br>
+</li>
+<li>--remove-INFO &lt;string&gt;<br>
+<li>--keep-INFO &lt;string&gt;<br>
+<br>
+These options are used to filter sites on the basis of INFO field flags. 
+The first option can be used to exclude sites with a specific INFO flag. 
+The second option can be used to select sites on the basis of specific INFO flags. These options can be used multiple times to specify multiple INFO flags. 
+The --keep-INFO option is applied before the --remove-INFO option. Note that <b>only INFO flags</b> can currently be used as filters 
+(i.e. there is currently no support for filtering by INFO field values). <br>
+<br>
+</li>
+<li>--minQ &lt;float&gt;<br>
+<br>
+Include only sites with Quality above this threshold.<br>
+<br>
+</li>
+<li>--min-meanDP &lt;float&gt;</li>
+<li>--max-meanDP &lt;float&gt;<br>
+<br>
+Include sites with mean Depth within the thresholds defined by these
+options.<br>
+<br>
+</li>
+<li>--maf &lt;float&gt;</li>
+<li>--max-maf &lt;float&gt;<br>
+<br>
+Include only sites with Minor Allele Frequency within the specified
+range.<br>
+<br>
+</li>
+<li>--non-ref-af &lt;float&gt;</li>
+<li>--max-non-ref-af &lt;float&gt;<br>
+<br>
+Include only sites with all Non-Reference Allele Frequencies within the specified
+range.<br>
+<br>
+</li>
+<li>--mac &lt;int&gt;</li>
+<li>--max-mac &lt;int&gt;<br>
+<br>
+Include only sites with Minor Allele Count within the specified
+range.<br>
+<br>
+</li>
+<li>--non-ref-ac &lt;float&gt;</li>
+<li>--max-non-ref-ac &lt;float&gt;<br>
+<br>
+Include only sites with all Non-Reference Allele Counts within the specified
+range.<br>
+<br>
+</li>
+<li>--hwe &lt;float&gt;<br>
+<br>
+Assesses sites for Hardy-Weinberg Equilibrium using an exact test, as
+defined by Wigginton, Cutler and Abecasis (2005). Sites with a p-value
+below the threshold defined by this option are taken to be out of HWE,
+and therefore excluded.<br>
+<br>
+</li>
+<li>--geno &lt;float&gt;<br>
+<br>
+Exclude sites on the basis of the proportion of missing data (defined
+to be between 0 and 1, where 1 indicates no missing data allowed).<br>
+<br>
+</li>
+<li>--max-missing-count &lt;int&gt;<br>
+<br>
+Exclude sites with more than this number of missing chromosomes.<br>
+<br>
+</li>
+<li>--min-alleles &lt;int&gt;</li>
+<li>--max-alleles &lt;int&gt;<br>
+<br>
+Include only sites with a number of alleles within the specified range.
+For example, to include only bi-allelic sites, one could use:<br>
+<br>
+<p class="codebox">vcftools --vcf file1.vcf --min-alleles 2 --max-alleles 2
+</p>
+<br><br>
+</li>
+<li>--thin &lt;int&gt;<br>
+<br>
+Thin sites so that no two sites are within the specified distance.<br>
+<br>
+</li>
+
+<li>--mask &lt;filename&gt;<br>
+<li>--invert-mask &lt;filename&gt;<br>
+<li>--mask-min &lt;int&gt;<br>
+<br>
+Include sites on the basis of a FASTA-like file. The provided file contains a sequence of integer digits (between 0 and 9) for each position on a chromosome that specify if a site at that position 
+should be filtered or not. An example mask file would look like:<br>
+<p class="codebox">&gt;1<br>0000011111222... </p>
+In this example, sites in the VCF file located within the first 5 bases of the start of chromosome 1 would be kept, whereas sites at position 6 onwards would be filtered out.
+The threshold integer that determines if sites are filtered or not is set using the --mask-min option, which defaults to 0. 
+The chromosomes contained in the mask file must be sorted in the same order as the VCF file. 
+The --mask option is used to specify the mask file to be used, whereas the --invert-mask option can be used to specify a mask file that will be inverted before being applied.
+<br>
+</li>
+
+</ul>
+</div>
+<div class="item">
+<h1><a name="indv_filter" class="Q">Individual Filters</a></h1>
+<ul>
+<li>--indv &lt;string&gt;<br>
+<br>
+Specify an individual to be kept in the analysis. This option can be used multiple times
+to specify multiple individuals.
+<br><br>
+</li>
+<li>--keep &lt;filename&gt;<br>
+<br>
+Provide a file containing a list of individuals to include in
+subsequent analysis. Each individual ID (as defined in the VCF
+headerline) should be included on a separate line.<br>
+<br>
+</li>
+<li>--remove-indv &lt;string&gt;<br>
+<br>
+Specify an individual to be removed from the analysis. This option can be used multiple times
+to specify multiple individuals. If the --indv option is also specified, then the --indv option is
+executed before the --remove-indv option.
+<br><br>
+</li>
+<li>--remove &lt;filename&gt;<br>
+<br>
+Provide a file containing a list of individuals to exclude in
+subsequent analysis. Each individual ID (as defined in the VCF
+headerline) should be included on a separate line. If both the --keep
+and the --remove options are used, then the --keep option is execute before
+the --remove option.<br>
+<br>
+</li>
+<li>--min-indv-meanDP &lt;float&gt;</li>
+<li>--max-indv-mean-DP &lt;float&gt;<br>
+<br>
+Calculate the mean coverage on a per-individual basis. Only individuals
+with coverage within the range specified by these options are included
+in subsequent analyses.<br>
+<br>
+</li>
+<li>--mind &lt;float&gt;<br>
+<br>
+Specify the minimum call rate threshold for each individual. <br>
+<br>
+</li>
+<li>--phased<br>
+<br>
+First excludes all individuals having all genotypes unphased, and <span style="text-decoration: underline;">subsequently excludes
+all sites with unphased genotypes</span>. The remaining
+data&nbsp;therefore consists of&nbsp;phased data only.
+</li>
+<li>--max-indv &lt;int&gt;<br>
+<br>
+Randomly thins individuals so that only the specified number are retained.
+</li>
+</ul>
+</div>
+<div class="item">
+<h1><a name="geno_filter" class="Q">Genotype Filters</a></h1>
+<ul>
+<li>--remove-filtered-geno-all</li>
+<li>--remove-filtered-geno &lt;string&gt;<br>
+<br>
+The first option removes all genotypes with a FILTER flag. The second option can be used to exclude genotypes with a specific filter flag.<br>
+<br>
+</li>
+<li>--minGQ &lt;float&gt;<br>
+<br>
+Exclude all genotypes with a quality below the threshold specified by
+this option (GQ).<br>
+<br>
+</li>
+<li>--minDP &lt;float&gt;<br>
+<br>
+Exclude all genotypes with a sequencing depth below that specified by
+this option (DP)</li>
+</ul>
+</div>
+<div class="item">
+<h1><a name="stats" class="Q">Output Statistics</a></h1>
+<ul>
+<li>--freq</li>
+<li>--counts</li>
+<li>--freq2</li>
+<li>--counts2<br>
+<br>
+Output per-site frequency information. The --freq outputs the allele frequency in a 
+file with the suffix '.frq'. The --counts option outputs a similar file with the suffix '.frq.count', 
+that contains the raw allele counts at each site.<br>
+The --freq2 and --count2 options are used to suppress allele information in the output file. In this case, 
+the order of the freqs/counts depends on the numbering in the VCF file.<br>
+<br>
+</li>
+<li>--depth<br>
+<br>
+Generates a file containing the mean depth per individual. This file
+has the suffix '.idepth'.<br>
+<br>
+</li>
+<li>--site-depth</li>
+<li>--site-mean-depth<br>
+<br>
+Generates a file containing the depth per site. The --site-depth option
+outputs the depth for each site summed across individuals. This file
+has the suffix '.ldepth'. Likewise, the --site-mean-depth outputs the
+mean depth for each site, and the output file has the suffix
+'.ldepth.mean'.<br>
+<br>
+</li>
+<li>--geno-depth<br>
+<br>
+Generates
+a (possibly very large) file containing the depth for each genotype in
+the VCF file. Missing entries are given the value -1. The file has the suffix '.gdepth'.<br>
+<br>
+</li>
+<li>--site-quality<br>
+<br>
+Generates a file containing the per-site SNP quality, as found in the QUAL column of the VCF file. This file
+has the suffix '.lqual'.<br>
+<br>
+</li>
+<li>--het<br>
+<br>
+Calculates
+a measure of heterozygosity on a per-individual basis. Specfically, the
+inbreeding coefficient, F, is estimated&nbsp;for each individual
+using
+a method of moments. The resulting file has the suffix '.het'.<br>
+<br>
+</li>
+<li>--hardy<br>
+<br>
+Reports a p-value for each&nbsp;site from a&nbsp;Hardy-Weinberg
+Equilibrium&nbsp;test (as
+defined by Wigginton, Cutler and Abecasis (2005)). The resulting file
+(with suffix '.hwe') also contains the Observed numbers of Homozygotes
+and Heterozygotes and the corresponding&nbsp;Expected numbers under
+HWE.&nbsp;<br>
+<br>
+</li>
+<li>--missing<br>
+<br>
+Generates
+two files reporting the missingness on a per-individual and per-site
+basis. The two files have suffixes '.imiss' and '.lmiss' respectively.<br>
+<br>
+</li>
+<li>--hap-r2</li>
+<li>--geno-r2</li>
+<li>--ld-window &lt;int&gt;</li>
+<li>--ld-window-bp &lt;int&gt;</li>
+<li>--min-r2 &lt;float&gt;<br>
+<br>
+These options are used to report Linkage Disequilibrium (LD) statistics
+as summarised by the r<sup>2</sup>, D, and D' statistics. The --hap-r2
+option informs vcftools to output a file reporting the r<sup>2</sup>, D, and D'
+statistics using phased haplotypes. These are the traditional measures of LD often reported in the population genetics literature. 
+If phased haplotypes are unavailable then the --geno-r2 option may be used, which calculates the squared correlation coefficient
+between genotypes encoded as 0, 1 and 2 to represent the number of non-reference alleles in each individual. This is the same as the LD measure reported by PLINK. The D and D' statistics are only available for phased genotypes.
+The haplotype version outputs a file with the suffix '.hap.ld', whereas the genotype version outputs a file with the suffix '.geno.ld'. The haplotype version implies the option --phased.
+<br><br>The --ld-window option defines the maximum number of SNPs between the SNPs being tested for LD.
+Likewise, the --ld-window-bp option can be used to define the maximum 
+physical separation (in base-pairs) of SNPs included in the LD calculation. Finally,
+the --min-r2 sets a minimum value for&nbsp;r<sup>2</sup>
+below which the LD statistic is not reported.<br>
+<br>
+</li>
+<li>--SNPdensity &lt;int&gt;<br>
+<br>
+Calculates the number and density of SNPs in bins of size defined by
+this option. The resulting output file has the suffix '.snpden'.<br>
+<br>
+</li>
+<li>--TsTv &lt;int&gt;<br>
+<br>
+Calculates the Transition / Transversion ratio in bins of size defined by
+this option. Only uses bi-allelic SNPs. The resulting output file has the suffix '.TsTv'. A summary is also supplied in a file with the suffix '.TsTv.summary'.<br>
+<br>
+</li>
+<li>--TsTv-by-count<br>
+<br>
+Calculates the Transition / Transversion ratio as a function of alternative allele count. Only uses bi-allelic SNPs. 
+The resulting output file has the suffix '.TsTv.count'. <br>
+<br>
+</li>
+<li>--TsTv-by-qual<br>
+<br>
+Calculates the Transition / Transversion ratio as a function of SNP quality threshold. Only uses bi-allelic SNPs. 
+The resulting output file has the suffix '.TsTv.qual'. <br>
+<br>
+</li>
+<li>--FILTER-summary<br>
+<br>
+Generates a summary of the number of SNPs and Ts/Tv ratio for each FILTER category. The output file 
+has the suffix '.FILTER.summary. <br>
+<br>
+</li>
+<li>--filtered-sites<br>
+<br>
+Creates two files listing sites that have been kept or removed after filtering. The first file, with
+suffix '.kept.sites', lists sites kept by vcftools after filters have been applied. The second file,
+with the suffix '.removed.sites', list sites removed by the applied filters.<br>
+<br>
+</li>
+<li>--singletons<br>
+<br>
+This option will generate a file detailing the location of singletons,
+and the&nbsp;individual they occur in. The file reports both true
+singletons, and private doubletons (i.e. SNPs where the minor allele
+only occurs in a single individual and that individual is homozygotic
+for that allele). The output file has the suffix '.singletons'.<br>
+<br>
+</li>
+<li>--site-pi</li>
+<li>--window-pi &lt;int&gt;<br>
+<br>
+These options are used to estimate levels of <a href="http://en.wikipedia.org/wiki/Nucleotide_diversity">nucleotide diversity</a>. The first
+option does this on a per-site basis, and the output file has the suffix '.sites.pi'. The second option calculates the nucleotide diversity
+in windows, with the window size defined in the option argument. <br>
+<br>
+</li>
+</ul>
+</div>
+<div class="item">
+<h1><a name="other_format" class="Q">Output in Other Formats</a></h1>
+<ul>
+<li>--012<br>
+<br>
+This option outputs the genotypes as a large matrix. Three files are
+produced. The first, with suffix '.012', contains the genotypes of each
+individual on a separate line. Genotypes are represented as 0, 1 and 2,
+where the number represent that number of non-reference alleles. Missing 
+genotypes are represented by -1. The second file, with suffix '.012.indv' 
+details the individuals included in the main file. The third file, with 
+suffix '.012.pos' details the site locations included in the main file.<br>
+<br>
+</li>
+<li>--IMPUTE<br>
+<br>
+This option outputs phased haplotypes in <a href="http://mathgen.stats.ox.ac.uk/impute/impute.html">IMPUTE</a>
+reference-panel format. As IMPUTE requires phased data, using this
+option also implies --phased. Unphased individuals and genotypes are
+therefore excluded. Only bi-allelic sites are included in the output. Using this option generates three files. The IMPUTE
+haplotype file has the suffix '.impute.hap', and the IMPUTE legend file
+has the suffix '.impute.hap.legend'. The third file, with suffix
+'.impute.hap.indv', details the individuals included in the haplotype
+file, although this file is not needed by IMPUTE.<br>
+<br>
+</li>
+<li>--ldhat<br>
+<li>--ldhat-geno<br>
+<br>
+These options output data in <a href="http://www.stats.ox.ac.uk/%7Emcvean/LDhat/">LDhat</a>
+format. Use of these options &nbsp;also require the --chr option to
+by used. The --ldhat option outputs phased data only, and therefore also implies --phased, leading to unphased
+individuals and genotypes being excluded. Alternatively, the --ldhat-geno option treats all of the data as unphased, and therefore
+outputs LDhat files in genotype/unphased format. In either case, two files are
+generated with the suffixes '.ldhat.sites'
+and '.ldhat.locs', which correspond to the
+LDhat 'sites' and 'locs' input files respectively.<br>
+<br>
+</li>
+<li>--BEAGLE-GL<br>
+<br>
+This option outputs genotype likelihood information for input into the 
+<a href="http://faculty.washington.edu/browning/beagle/beagle.html">BEAGLE</a> program. 
+This option requires the VCF file to contain the FORMAT GL tag, which can generally be output by 
+SNP callers such as <a href="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit">the GATK</a>. 
+Use of this option requires a chromosome to be specified via the --chr option. The resulting output 
+file (with the suffix '.BEAGLE.GL') contains genotype likelihoods for biallelic sites, and is 
+suitable for input into BEAGLE via the 'like=' argument.<br>
+<br>
+</li>
+<li>--plink<br>
+<br>
+This option outputs the genotype data in <a href="http://pngu.mgh.harvard.edu/%7Epurcell/plink/">PLINK</a>
+PED format. Two files are generated, with suffixes '.ped' and '.map'. Note that only bi-allelic loci will be output.
+Further details of these files can be found in the <a href="http://pngu.mgh.harvard.edu/%7Epurcell/plink/data.shtml#ped">PLINK
+documentation</a>. <br>
+<br>Note: This option can be very slow on large datasets. Using the --chr option to divide up the dataset is advised.<br>
+<br>
+</li>
+<li>--plink-tped<br>
+<br>
+The --plink option above can be extremely slow on large datasets. An alternative that might be considerably quicker is 
+to output in the <a href="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr">PLINK transposed format</a>. 
+This can be achieved using the --plink-tped option, which produces two files with suffixes '.tped' and '.tfam'.
+<br>
+<br>
+</li>
+<li>--recode<br>
+<br>
+The --recode option is used to generate a VCF file from the input VCF file
+having applied the options specified by the user. The output file has
+the suffix '.recode.vcf'. 
+<br><br>
+By default, the INFO fields are removed from the output file, as the INFO values may be invalidated 
+by the recoding (e.g. the total depth may need to be recalculated if individuals are removed). 
+This default functionality can be overridden by using the --recode-INFO &lt;string&gt; option, where &lt;string&gt;
+defines the INFO key to keep in the output file. The --recode-INFO flag can be used multiple times. 
+Alternatively, the option --recode-INFO-all can be used to retain all INFO fields.
+</li>
+</ul>
+</div>
+<div class="item">
+<h1><a name="misc" class="Q">Miscellaneous</a></h1>
+<ul>
+<li>--extract-FORMAT-info &lt;string&gt;<br>
+<br>
+Extract information from the genotype fields in the VCF file relating to a specfied FORMAT identifier. For example,
+using the option '--extract-FORMAT-info GT' would extract the all of the GT (i.e. Genotype) entries. 
+The resulting output file has the suffix '.&lt;FORMAT_ID&gt;.FORMAT'.
+<br>
+<br>
+<li>--get-INFO &lt;string&gt;<br>
+<br>
+This option is used to extract information from the INFO field in the
+VCF file. The &lt;string&gt; argument specifies the INFO tag to
+be extracted, and the option can be used multiple times in order to
+extract multiple INFO entries. The resulting file, with suffix '.INFO',
+contains the required INFO information in a tab-separated table. For
+example, to extract the NS and DB flags, one would use the command:
+<br>
+<br>
+<p class="codebox">vcftools --vcf file1.vcf --get-INFO NS --get-INFO DB </p>
+<br>
+</li>
+</ul>
+</div>
+
+<div class="item">
+<h1><a name="diff" class="Q">VCF File Comparison Options</a></h1>
+<p><b>The file comparison options are currently in a state of flux and likely buggy. If you find a bug,
+ please report it. Note that genotype-level filters are not supported in these options.</b><br>
+</p>
+<ul>
+<li>--diff &lt;filename&gt;<br>
+<li>--gzdiff &lt;filename&gt;<br>
+<br>
+Select a VCF file for comparison with the file specified by the --vcf option. Outputs two files 
+describing the sites and individuals common / unique to each file. These files have the suffixes 
+'.diff.sites_in_files' and '.diff.indv_in_files' respectively. The --gzdiff version can be used to 
+read compressed VCF files.
+<br><br>
+</li>
+<li>--diff-site-discordance<br>
+<br>
+Used in conjuction with the --diff option to calculate discordance on a site by site basis. The 
+resulting output file has the suffix '.diff.sites'.
+<br><br>
+</li>
+<li>--diff-indv-discordance<br>
+<br>
+Used in conjuction with the --diff option to calculate discordance on a per-individual basis. The 
+resulting output file has the suffix '.diff.indv'.
+<br><br>
+</li>
+<li>--diff-discordance-matrix<br>
+<br>
+Used in conjuction with the --diff option to calculate a discordance matrix. This option only works 
+with bi-allelic loci with matching alleles that are present in both files. The resulting output file 
+has the suffix '.diff.discordance.matrix'.
+<br><br>
+</li>
+<li>--diff-switch-error<br>
+<br>
+Used in conjuction with the --diff option to calculate phasing errors 
+(specifically '<a href="http://www.cell.com/AJHG/retrieve/pii/S0002929707619788">switch errors</a>'). 
+This option generates two output files describing switch errors found between sites, and the average switch 
+error per individual. These two files have the suffixes '.diff.switch' and '.diff.indv.switch' respectively. 
+<br><br>
+</li>
+
+</ul>
+</div>
+
+<div class="item">
+<h1><a name="development" class="Q">Options still in development</a></h1>
+<p>The following options are yet to be finalised, are likely to contain bugs, and are likely to change in the future.<br>
+</p>
+<ul>
+<li>--fst &lt;filename&gt;<br>
+<li>--gzfst &lt;filename&gt;<br>
+<br>
+Calculate F<sub>ST</sub> for a pair of VCF files, with the second file being specified by this option. 
+F<sub>ST</sub> is currently calculated using the formula described in the supplementary material of the <a href="http://www.ncbi.nlm.nih.gov/pubmed/16255080">Phase I HapMap paper</a>.
+Currently, only pairwise F<sub>ST</sub> calculations are supported, although this will likely change in the future. 
+The --gzfst option can be used to read compressed VCF files. 
+This option is likely to be depreciated in future releases, and it is recommended that you use the --fst-pop option instead.
+<br>
+<br>
+</li>
+<li>--fst-pop &lt;filename&gt;<br>
+<br>
+If you do not have separate files for each population, you can use this option to calculate F<sub>ST</sub>. 
+This option is used to provide a file which lists the individuals in each population, and is used multiple times to specific multiple populations.
+Unlike the --fst option, this option can be used to calculate F<sub>ST</sub> for more than two populations. 
+<br>
+<br>
+</li>
+<!--
+<li>--pca <br>
+<br>
+Perform Principal Component Analysis.
+<br>
+<br>
+</li>
+-->
+<li>--LROH <br>
+<br>
+Identify Long Runs of Homozygosity.
+<br>
+<br>
+</li>
+<li>--relatedness <br>
+<br>
+Output Individual Relatedness Statistics.
+<br>
+<br>
+</li>
+<li>--TajimaD <int> <br>
+<br>
+Output Tajima's D statistic in bins of size <int>.
+<br>
+<br>
+</li>
+</ul>
+</div>
+