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= Options =
= Options =
== allelefrequency ==
== --allelefrequency ==
Option to calculate allele frequency and output to prefix.freq. <br>
Option to calculate allele frequency and output to prefix.freq. <br>
== allelecounts ==
== --allelecounts ==
Option to calculate allele counts and output to prefix.ac. <br>
Option to calculate allele counts and output to prefix.ac. <br>
== ld ==
== --ld ==
Option to calculate LD. Note that this option has to be turned on for LD to be calculated. <br>
Option to calculate LD. Note that this option has to be turned on for LD to be calculated. <br>
== windowSize ==
== --windowSize ==
Option to specify the # of flanking SNPs with which LD values are calculated for each SNP. Default is 1,000, meaning that LD with 1,000 SNPs on each side (2,000 total) will be calculated for each SNP. <br>
Option to specify the # of flanking SNPs with which LD values are calculated for each SNP. Default is 1,000, meaning that LD with 1,000 SNPs on each side (2,000 total) will be calculated for each SNP. <br>
== r2Threshold ==
== --r2Threshold ==
Minimum r2 value for a pair of SNPs to be in output. Default is 0.00. <br>
Minimum r2 value for a pair of SNPs to be in output. Default is 0.00. <br>
== DprimeThreshold ==
== --DprimeThreshold ==
Minimum D' value for a pair of SNPs to be in output. Default is 0.00. <br>
Minimum D' value for a pair of SNPs to be in output. Default is 0.00. <br>
== pairWithSNP ==
== --pairWithSNP ==
Option to calcuate LD only with a particular SNP. <br>
Option to calcuate LD only with a particular SNP. <br>
== pairWithList ==
== --pairWithList ==
A list of SNPs with which LD values will be calculated. <br>
A list of SNPs with which LD values will be calculated. <br>
== coupling ==
== --coupling ==
Option to output for each pair the alleles that are positively correlated. <br>
Option to output for each pair the alleles that are positively correlated. <br>
== prefix ==
== --prefix ==
Option to specify output prefix. <br>
Option to specify output prefix. <br>
sample.freq <br>
sample.freq <br>
SNP AL1 AL2 Freq1 MAF<br>
chr12:16099 1 3 0.4000 0.4000<br>
chr12:16163 4 2 0.9000 0.1000<br>
rs7358779 2 3 0.1000 0.1000<br>
chr12:17063 1 3 0.8000 0.2000<br>
...<br>
<br>
== .ac ==
== .ac ==
Generated when option --allelecounts is turned on. <br> <br>
Generated when option --allelecounts is turned on. <br> <br>
sample.ac <br>
sample.ac<br>
SNP AL1 AL2 AC1 MAC<br>
chr12:16099 1 3 4 4<br>
chr12:16163 4 2 9 1<br>
rs7358779 2 3 1 1<br>
chr12:17063 1 3 8 2<br>
<br>
== .xt ==
== .xt ==
Generated when option --ld is turned on. <br> <br>
Generated when option --ld is turned on. <br> <br>
sample.xt<br>
M1 M2 DPRIME DELTASQ COUPLING<br>
chr12:16252 chr12:16585 1.0000 0.6667 2,1<br>
chr12:16252 chr12:16665 1.0000 1.0000 2,3<br>
chr12:16252 chr12:16693 1.0000 1.0000 2,4<br>
...<br>
<br>
= download =
= download =
