KSNP: k-mer based haplotype assembly

Download and install

Dependencies

• cmake >= 3.10
• gcc >= 6.4
• zlib >= 1.2
• samtools >= 1.9

git clone https://github.com/zhouqiansolab/KSNP-k-mer-based-haplotype-assembly.git
cd KSNP-k-mer-based-haplotype-assembly;
mkdir build; cd build
cmake ..; make

Usage

samtools view in.bam chr_name | ksnp -k <k-mer size> -v <VCF file> -o <output file>
  ## K-mer size supports INT value from 2 to 10 (default value is 2)
  ## The in.bam is sorted and indexed. The chr_name is not required when the in.bam only includes one chromosome.
  ## The VCF file should contain SNP positions on one chromosome. Please split the VCF file into small files according to the chr_name. The VCF file can be in be in compressed gz format or decompressed format.
  ## The output file includes all of the variants in input VCF file with phased information.
  

Contact

zhouqian_solab@163.com