|
Haploview can be run from the command line without the display in order to do processing of multiple datasets or quick computation on very large datasets. In order to run Haploview without the display, add the "-nogui" flag. The "-help" flag shows a condensed explanation of all the command line options explained below. Haploview can be run from the command line using:
java -jar Haploview.jar
- -h, -help
Print help information.
- -n, -nogui
Command line mode—does not launch display.
- -q, -quiet
Quiet mode—minimizes output to command line.
- -log <filename>
Outputs logfile information to specified filename (defaults to haploview.log if no name specified)
- -out <fileroot>
Specify a fileroot to be used for all output files
- -memory <memsize>
Allocate <memsize> megabytes of memory to the Haploview process (default is 512MB).
- -pedfile <filename>
Specify a genotype input file (or http:// location) in pedigree format. This option works in GUI mode.
- -hapmap <filename>
Specify a HapMap format input file (or http:// location). This option works in GUI mode.
- -phasedhmpdata <filename>
Specify a PHASE format data input file (or http:// location). This option works in GUI mode.
- -phasedhmpsample <filename>
Specify a PHASE format sample input file (or http:// location). This option works in GUI mode.
- -phasedhmplegend <filename>
Specify a PHASE format legend input file (or http:// location). This option works in GUI mode.
- -hapmapDownload
Specify a phased HapMap download. This option works in GUI mode.
- -haps <filename>
Specify a phased input file (or http:// location). This option works in GUI mode.
- -info <filename>
Specify a marker information file (or http:// location). This option works in GUI mode.
- -plink <filename>
Specify a PLINK or other results file (or http:// location). This option only works in GUI mode.
- -map <filename>
Specify a map or binary map file (or http:// location). This option only works in GUI mode.
- -batch <filename>
Specify a batch load file.
- -blocks <filename>
Specify a block definition file (or http:// location). This will automatically use this block definition for haplotype output.
- -track <filename>
Specify an analysis track file (or http:// location)
- -chromosome <1-22,X,Y>
Specify which chromosome these data come from. This is especially critical when analyzing data from the X chromosome or direct HapMap downloads.
- -panel <CEU,YRI,CHB+JPT>
Specify which analysis panel to use for phased HapMap downloads.
- -startpos <integer>
Specify the start position in kb for phased HapMap downloads.
- -endpos <integer>
Specify the end position in kb for phased HapMap downloads.
- -release <16a,21,22>
Specify the HapMap release version for phased HapMap downloads (defaults to 21).
- -gzip
Specify PHASE format inputs using GZIP compression
- -nonSNP
Specify that the accompanying PLINK file is non-SNP based output. This option only works in GUI mode.
- -selectCols
Activate the preloading column filter for PLINK loads. This option only works in GUI mode.
- -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.
- -blockoutput <type>
Generate haplotypes and population frequencies for blocks of <type>, which can be GAB (Gabriel et al), GAM (4 gamete blocks), SPI (solid spine blocks) or ALL (each of the previous 3). The default block type is Gabriel. More information can be found with the blocks help.
- -blockCutHighCI <thresh>
Gabriel 'Strong LD' high confidence interval D' cutoff.
- -blockCutLowCI <thresh>
Gabriel 'Strong LD' low confidence interval D' cutoff.
- -blockMAFThresh <thresh>
Gabriel MAF threshold. Markers below this allele frequency will be skipped in building Gabriel blocks.
- -blockRecHighCI <thresh>
Gabriel recombination high confidence interval D' cutoff.
- -blockInformFrac <thresh>
Gabriel fraction of informative markers required to be in strong LD.
- -block4GamCut <thresh>
4 Gamete block cutoff for frequency of 4th pairwise haplotype.
- -blockSpineDP <thresh>
Solid Spine blocks D' cutoff for 'Strong LD'.
- -check
Output marker quality checks to <inputfile>.CHECK
- -mendel
Output Mendel error information to <inputfile>.MENDEL
- -malehets
Output chromosome X male heterozygote information to <inputfile>.MALEHETS
- -dprime
Output pairwise LD text table to <inputfile>.LD. Note that -dprime and -check default to no haplotype output unless the -blockoutput flag is also specified.
- -png
Output PNG image file of LD display to <inputfile>.LD.PNG
- -compressedpng
Output low-resolution (smaller file) PNG image of LD display to <inputfile>.LD.PNG
- -svg
Output svg format of LD display to <inputfile>.LD.SVG
- -infoTrack
Include HapMap info track in PNG image outputs
- -spacing <threshold>
Use proportional spacing for dumped LD pngs. <threshold> ranges from 0 (no spacing) to 1 (max spacing) with a default of 0.
- -ldcolorscheme <type>
Use a particular color scheme for dumped LD pngs. <type> can be DEFAULT, RSQ, DPALT, GAB or GAM. More information can be found with the LD display help
- -hapthresh <threshold>
Only output haplotypes with frequency ≥ <threshold>. Note that multiallelic D' and htSNPs are computed using only displayed haplotypes.
- -excludeMarkers <markers>
Exclude markers in a comma separated list with ranges specified as start..end. So, to exclude markers 3, 5 and 10 through 15 you'd use "-excludeMarkers 3,5,10..15"
- -assocCC
Output case/control association results. Saves single marker results to <inputfile>.ASSOC and haplotype results to <inputfile>.HAPASSOC. Haplotype association results are not generated if block type is set to ALL.
- -assocTDT
Output TDT association results. Saves single marker results to <inputfile>.ASSOC and haplotype results to <inputfile>.HAPASSOC. Haplotype association results not generated if block type is set to ALL.
- -customAssoc <file>
Loads a set of custom tests for association.
- -permtests <numtests>
Performs <numtests> permutations on default association tests (or custom tests if a custom association file is specified) and writes to <inputfile>.PERMUT
- -pairwiseTagging
Generates pairwise tagging information in <inputfile>.TAGS and .TESTS
- -aggressiveTagging
As above but generates 2-marker haplotype tags unless specified otherwise by -aggressiveNumMarkers
- -tagrsqcounts
Generates conditional haplotype probabilities from tagger in <inputfile>.CHAPS
- -aggressiveNumMarkers <2,3>
Specifies whether to use 2-marker haplotype tags or 2 and 3-marker haplotype tags.
- -maxNumTags <n>
Only selects <n> best tags.
- -includeTags <markers>
Forces in a comma separated list of marker names as tags.
- -includeTagsFile <file>
Forces in a file (or http:// location) of one marker name per line as tags.
- -excludeTags <markers>
Excludes a comma separated list of marker names from being used as tags.
- -excludeTagsFile <file>
Excludes a file (or http:// location) of one marker name per line from being used as tags.
- -captureAlleles <file>
Capture only the alleles contained in a file (or http:// location) of one marker name per line.
- -designScores <file>
Specify design scores in a file (or http:// location) of one marker name and one score per line.
- -mindesignscore <threshold>
Specify a minimum design score threshold.
- -mintagdistance <distance>
Specify a minimum distance in bases between picked tags.
- -taglodcutoff <thresh>
Tagger LOD cutoff for creating multimarker tag haplotypes.
- -tagrsqcutoff <thresh>
Tagger r^2 cutoff.