H-PoPG

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H-PoP and H-PoPG: Heuristic Partitioning Algorithms for Single Individual Haplotyping of Polyploids

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# H-PoPG
H-PoP and H-PoPG:  Heuristic Partitioning Algorithms for Single Individual Haplotyping of Polyploids

Usage: 
       java -jar H-PoPG.jar -p k-ploidy w weight (default 0.9) -f input_SNP_matrix_file_name -vcf vcf_file_name  -o output_phased_haplotypes_file_name

If -vcf option and the vcf file name are provided, H-PoPG is called, otherwise H-PoP is called.

For example: 
(1)  java -jar H-PoPG.jar -p 3 -f frags.txt -o phased_haplotypes.txt
   The command will call the algorithm H-PoP to reconstruct the haplotypes for a triploid (k=3). 
   The input SNP matrix is provided by the file frags.txt.  
   The reconstructed three haplotypes are stored in the output file phased_haplotypes.txt.

(2) java -jar H-PoPG.jar -p 3 -f frags.txt -vcf example.vcf -o phased_haplotypes.txt
   The command will call the algorithm H-PoPG to reconstruct the haplotypes for a triploid (k=3)
   The genotype informaion is provided by the input file example.vcf
   
Input SNP matrix files uses a space(or tab) delimited file format with aligned SNP reads separated by new lines. 
The columns are specified as follows:

column 1: the number of read blocks (consecutive 0 1 sequence separated by a gap (i.e. a sequence of -))

column 2: read name

column 3: the start position of the first block

column 4: the 0 1 sequence of the first block

If there are more than 1 blocks, additional column pairs like columns 3 and 4 are needed for additional blocks.

the last column: 
the sequence encoding the quality values for the sequence of all blocks, and must contain the same number of symbols as the total number of 0 and 1 of the read.

Example of input_SNP_matrix_file:

1 read_1 23 0101 G,&G

1 read_2 24 0011 HGGG

4 read_3 25 0 26 10 29 0 31 1 GGGGG

2 read_4 26 00011 40 11100 GGGGGGGGGG

If a VCF file is provided, the start position of a read block _MUST_ match the index of the corrsponding SNP in the VCF file.

Please see the example files frags.txt, example.vcf and phased_haplotypes.txt
for the formats of the input SNP matrix file , genotype file and the output file .

There is a discussion about the problems of using H-PoPG in stackoverflow (Thank Mel Carbajo for starting the discussion), and if you have any problems about using H-PoPG, please join the discussion. 
http://stackoverflow.com/questions/39859409/h-popg-haplotyper-nullpointerexception-error-at-algorithms-hbop2builder

*****Version 0.2.0 updated on Oct. 18, 2019*****

H-PoPG version: 0.2.0. Author: Xie Minzhu. Email: xieminzhu@hotmail.com

(1) Without -a option, the polyplotyping algorithm called is H-PoP or H-PoPG according to whether a vcf is provided.

Usage: 
  
    java -jar H-PoPGv0.2.0.jar [-p ploidy (default is 3) -m maxsize (default is ploidy*ploidy*10) -w weight (default is 0.9)] -v[cf] vcffilename -b[am] bamfilenme [-f[rag] alignedFragsFileName].. -o outputPhasedFilename
      
    java -jar H-PoPGv0.2.0.jar [-p ploidy (default is 3) -m maxsize (default is ploidy*ploidy*10) -w weight (default is 0.9)] -f[rag] alignedFragsFileName [-f[rag] alignedFragsFileName].. [-v[cf] vcffilename] -o outputPhasedFilename

(2) With the option "-a HapTree", HapTree is called. (HapTree_v0 should be placed at the same directory as this java package.)

Usage: 
  
    java -jar H-PoPGv0.2.0.jar -a HapTree [-p ploidy (default is 3) -v[cf] vcffilename -b[am] bamfilenme [-f[rag] alignedFragsFileName].. -o outputPhasedFilename
      
    java -jar H-PoPGv0.2.0.jar -a HapTree [-p ploidy (default is 3)] -v[cf] vcffilename -f[rag] alignedFragsFileName [-f[rag] alignedFragsFileName].. -o outputPhasedFilename

(3) Only transfer a BAM File to a Frag file (the read covering less than 2 SNPs are discarded):

java -jar H-PoPGv0.2.0.jar -v[cf] vcffilename -b[am] bamfilenme -o outputFragFilename -b2f

(4) Output a File with detailed information about position in genome, SNP id, SNP alleles of the phased haplotypes, use the option -detailedoutput or -d as follows:

java -jar H-PoPGv0.2.0.jar [-p ploidy (default is 3) -m maxsize (default is ploidy*ploidy*10) -w weight (default is 0.9)] -v[cf] vcffilename -b[am] bamfilenme [-f[rag] alignedFragsFileName].. -d[etailedoutput] outputdetailedPhasedFilename

(5) Print this help information:

java -jar H-PoPGv0.2.0.jar -h

Note: 
 
    (1) If a BAM File has been provide, a VCF file is needed. The input files can include multiple Frag Files, one Bam file and one VCF file.
    
    (2) For case (4), the vcf file must be provided.

H-PoPG

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