traxexx / lhmei_v4 Goto Github PK

Usage: [] is default. Please pecify those * options.
    Use -h to show advanced options.
    Test:  Run test commands. Override all single dash options.

 *  -Bam:  Raw bam files for LHMEI discovery. MUST be sorted by cooridinate.
 *  -WorkDir:  Working directory (if not exist, LHMEI will create one).
 *  -Mapper:  Mapper used to generate the raw bam. If not installed globally, please specify path. [/net/wonderland/home/mktrost/dev/gotcloud/bin/bwa-mem]
 *  -GenomeFasta: reference genome fasta. [ HOME hs37d5.fa]
    -Sample:  Sample name. [basename of -Bam]
    -Chr:  Chr to discover. -1 means whole genome. [-1]
    -Win:  Sliding window size in bp. [600]
    -Step:  Moving step of sliding window. [100]
    --verbose:  Print user defined options out. [off]
	

Default HetIndex:
   250 Alu
   200 L1
   100 SVA