HANDS2: accurate assignment of homoeallelic base-identity in allopolyploids despite missing data
Current version: HANDS2 v1.1.1 Assign homoeallelic base identities in allopolyploids using diploid similarity.
Usage: java -jar hands2.jar
Commands help : Display this help assign : Assign homoeallelic base identities coverage : Calculate the number of reads supporting a particular base at each position seq2ref : Create an in silico reference using a set of unigenes, contigs or other sequences
Command: assign - Assign homoeallelic base identities Usage: java -jar hands2.jar assign
Input Parameters -h or -help : Display this help -i : Polyploid SAM/BAM file -g : GFF3 file containing gene start/end coordinates -hsp : Polyploid HSP file in VCF Format. -snp : Diploid # n SNP file in VCF Format. -bc : Polyploid Base coverage file (optional). See coverage command. -bc : Diploid # n Base coverage file, e.g. bc1 (optional). See coverage command. -out : Sub-Genome # n output file, e.g. out1 -vcf : Generate VCF output (Default: TRUE). When FALSE, tab-delimited output is generated. -sp : SNP pair proportion threshold (Default: 0.05) -pm : Base pattern matching threshold (Default: 0.5) -pa : Base pattern assignment mode (M: Keep maximum proportion for a base or A: Add all proportions; Default: M) -r : Rectify Assignment using reference genome (Default: FALSE) -m : Merge Base Patterns before assignment (Default: FALSE) -u : Assign the unassigned base, if any, to the subgenome to which no base is assigned (Default: TRUE) -d : Use genome as distant genome (Default: ) Note: At most one diploid SNP file can be missing. Use "" for the missing file. HANDS2 supports up to 10 genomes.
Command: coverage - Calculate base coverage for each position from a SAM file Usage: java -jar hands2.jar coverage
Input Parameters -h or -help : Display this help -i : SAM/BAM file -o : Output file -q : Base quality threshold (Default: 20)
Command: seq2ref - Create an in silico reference from given sequences/contigs Usage: java -jar hands2.jar seq2ref
Input Parameters -h or -help : Display this help -i : Input sequence file (multifasta format) -o : Output file -n : Header for the in silico reference -g : Gap size between two sequences (Default: 200)