dwpeng / ksnp

KSNP: k-mer based haplotype assembly

Download and install

Dependencies

• cmake >= 3.10
• gcc >= 6.4
• htslib >= 1.15
• zlib >= 1.2

KSNP can be installed on Linux or MAC OS.

Install from conda

We recommend users install KSNP using conda command.

# New environment is recommended for avoiding dependency conflicts.
conda create -n ksnp_env
conda install -c conda-forge -c bioconda ksnp

Install from source

Before compile the KSNP code locally, keep sure the dependency htslib has been correctly installed. Please add the subdirectory containing libhts.so to the default environmental variable for searching dynamic-link libraries (such as LD_LIBRARY_PATH environment variable in Linux OS) or use the pre-compile option -DHTSLIB= when running cmake to specify the location.

git clone https://github.com/zhouqiansolab/KSNP.git
cd KSNP; mkdir build; cd build
cmake -DHSTLIB=<directory of libhts.so> ..
make

If the installation is successful, the build subdirectory will contain the executable file ksnp.

Usage

ksnp -k <k-mer size> -b <BAM> -r <FASTA> -v <VCF> -o <output file>  [-c chr]
  ## The k-mer size supports INT value from 2 to 5. Default value is set to 2.
  ## BAM file contains the aligned reads. It must be sorted and indexed.
  ## FASTA file is the reference sequence used for reads alignment and variants calling. It should be indexed by 'samtools faidx'
  ## Users may specify a chromosome using option -c <chr-name> to manually parallize KSNP across chromosomes.
  ## VCF file contains the heterozygous variants to phase. It should be properly filtered before phasing.
  ## The output file keeps all varinats in input VCF file but with phased information. Without specifying it, the results will be print to stdout.
  ## Sample usage: ksnp -b aln.bam -r ref.fa -v variants.vcf -o phased.vcf
  ## -c allows users to specify individual chromosome for phasing, enabling chromosome-level parallel processing without the need for splitting input files.

For testing

cd test
ksnp -k 2 -b aln.bam -r ref.fa -v variants.vcf -o test_ksnp.vcf

expect_output.vcf is an expected output file that can be used for comparing with the test results.

Contact

[email protected]