HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids
HANDS is depreciated. Please use HANDS2. HANDS v1.1 Usage: java -jar hands.jar Input Parameters -h or -help : Display this help -s : Polyploid SAM file -g : GFF file containing gene coordinates -hsp : Polyploid HSP file -snp : Diploid # n SNP file -bd : Polyploid Base Distribution File (Optional) -bd<1> : Diploid # n Base Distribution File (Optional) -out : Sub-Genome # n Output File -sp : SNP Pair Proportion Threshold (Default: 0.05) -pm : SNP Pattern Matching Threshold (Default: 0.5) -r : Rectify Assignment using Reference Genome (Default: FALSE) -d : Use Genome as Distant Genome (Default: ) Note: At most one Diploid SNP file can be missing. Use "" for the missing file. HANDS supports up to 10 genomes.