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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 or -w ==
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 or -t ==
Minimum r2 value for a pair of SNPs to be in output. Default is 0.00. <br>
Minimum r<sup>2</sup> value for a pair of SNPs to be in output. Default is 0.00. <br>
== --DprimeThreshold ==
== --DprimeThreshold or -d ==
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>
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 or -o ==
Option to specify output prefix. <br>
Option to specify output prefix. <br>
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...<br>
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== .ac ==
== .ac ==
= download =
= download =
You can download the source codes and example files [https://www.sph.umich.edu/csg/yli/haploxt_V108.tgz haploxt].
To install, simply type the following command:
./build.csh
= sample command line =
./haploxt_names -s sample.snps -h sample.hap --allelefreq --ld -w 500 -t 0.5 --coupling -o sample.out
= Additional Questions =
= Additional Questions =
Please email [mailto:yunli@med.unc.edu Yun Li].
Please email [mailto:yunli@med.unc.edu Yun Li].
