The bamtools are required to manually download while other programs are included.
Type make in the src direcotry
In the package folder, type ./Run_HapSV, and you will see the list of parameters
Version 1.1: released on May 22th, 2015
Usage: ./RunHapSV.sh -b <DIR> [OPTION]
-f <int> fasta of assembled contigs
-1 <int> fastq of 1st reads
-2 <int> fastq of 2nd reads
-z <int> insert size of paired-end reads
-v <int> standard deviation of insert size
-l <int> read length
-h help
For instance, given a contig file named "contig.fa" and fastq files of paried-end reads "R1.fq" and "R2.fq", simply type
./Run_HapSV -f contig.fa -1 R1.fq -2 R2.fq
The output files are stored in a folder named haplotype_result. If there are multiple chromosomes/contigs, each of them is stored in a separate subfolder. Within each chromosome/contig subfolder, there are multiple output files explained below.
The main output file similar to the standard vcf format yet including block boundaries and SV information. Each row stands for a SNP or SV. The haplotype blocks are represented with a dash line. The following example shows three haplotype blocks composed of 6 SNPs and one SV insertion. Each row contains the chr./contig ID, variation type (SNP, Ins, Del, Inv), position, size (of SV if it is), allele on 1st haplotype, allele on 2nd haplotype.
#ref_name type pos size hap0 hap1
contig1001 SNP 396 - G G
contig1001 SNP 405 - T T
contig1001 SNP 470 - G G
-
contig1001 SNP 5398 - C T
contig1001 Ins 5494 109 - V
contig1001 SNP 5565 - G A
-
contig1001 SNP 6380 - G A
This output file stores the simplifed representation of paternal/maternal haplotypes sequences over SNPs only. There are two lines storing the paternal and maternal haplotype sequences, where the haplotype block boundary is represented using vertical line. e.g., three haplotype blocks composed of 22 SNPs.
GTG|TCTCGTAATCACGATAGT|G
GTG|AGATAACGCGGTGATAGT|A
The loci of detected SNPs.
The loci of detected SVs.
The input SNP/SV matrix used in the constrained MEC model.