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Revision as of 17:47, 16 March 2018
, 17:47, 16 March 2018no edit summary
[[Category:RAREMETALWORKER]]
==Useful Links==
==Useful Links==
===--zip===
===--zip===
* By issuing --zip, RAREMETALWORKER compress the [[ RAREMETALWORKER#Summary_Statistics| '''summary statistics''']] and [[RAREMETALWORKER#LD_Matrices | '''LD matrices''']] generated automatically, using gzip.
* By issuing --zip, RAREMETALWORKER compress the [[ RAREMETALWORKER#Summary_Statistics| '''summary statistics''']] and [[RAREMETALWORKER#LD_Matrices | '''LD matrices''']] generated automatically, using gzip. And the output zip files will be indexed using tabix.
=== --thin ===
=== --thin ===
* --geneMap takes a string describing the path to find mapping file for manhattan plot annotation.
* --geneMap takes a string describing the path to find mapping file for manhattan plot annotation.
* The default is human genome build 19, saved in raremetal/data/refFlat_hg19.txt.
* The default is human genome build 19, saved in raremetal/data/refFlat_hg19.txt.
===--mergedVCFID===
* This options allows RAREMETALWORKER to recognize VCF samples IDs in "FAMID_PID" format.
* The default value is OFF, which means VCF sample IDs are consistent with PID field in PED file.
==PhoneHome==
==PhoneHome==
