From Genome Analysis Wiki
Jump to navigationJump to search
292 bytes added
, 17:47, 16 March 2018
Line 1: |
Line 1: |
| + | [[Category:RAREMETALWORKER]] |
| ==Useful Links== | | ==Useful Links== |
| | | |
Line 58: |
Line 59: |
| | | |
| ===--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 === |
Line 157: |
Line 158: |
| * --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== |