haploview画出所有SNP的LD关系图

有时候我们想画出所有SNP的LD关系图，则需要在命令行添加“-skipcheck”命令行，如下所示：

java -jar Haploview.jar -skipcheck -n -pedfile 800kb1.ped -info 800kb1.info -png -out 800kb

　这样就不需要经过haploview的过滤标准了。

如果只想过滤某个标准，则可参看下来参数

-skipcheck Skip all the genotype data quality checks and uses all markers for all
analyses.
-minMAF <threshold> Exclude all markers with minor allele frequency below <threshold>,
which must be between 0 and 0.5. Default of 0. This option works in
GUI mode.
-maxMendel <integer> Exclude markers with greater than <integer> Mendelian inheritance
errors. Default of 1. This option works in GUI mode.
-minGeno <threshold> Exclude markers with less than <threshold> fraction of nonzero
genotypes. <threshold> must be between 0 and 1 with a default of 0.5.
This option works in GUI mode.
-hwcutoff <threshold> Exclude markers with a Hardy Weinberg p-value less than
<threshold>, which ranges from 0 to 1 with a default of 0.001 This
option works in GUI mode.
-maxDistance <distance> Maximum intermarker distance for LD comparisons (in kilobases).
Default is 500. This option works in GUI mode.
-missingCutoff <threshold> Exclude individuals with more than <threshold> fraction missing data,
where <threshold> is a value between 0 and 1 with a default of 0.5.
This option works in GUI mode.