Genome preparation
Full list of options for SNPsplit_genome_preparation
Note
USAGE: SNPsplit_genome_preparation [options] --vcf_file <file> --reference_genome /path/to/genome/ --strain <strain_name>
--vcf_file <file>
Mandatory file specifying SNP information for mouse strains from the Mouse Genomes Project: v8 annotation file. The file used and approved is called mgp_REL2021_snps.vcf.gz. Please note that future versions of this file or entirely different VCF files might not work out-of-the-box but may require some tweaking. SNP calls are read from the VCF files, and high confidence SNPs are written into a folder in the current working directory called SNPs_<strain_name>/chr<chromosome>.txt, in the following format:
--v7_VCF
This will use the file mgp_REL2005_snps_indels.vcf.gz instead of the mgp v8 file mentioned above, for backward compatibility reasons. This file contains both SNP and INDEL information, but INDELs are skipped.
Note
NOTE: The v5 and v7 files work for the GRCm38 (now outdated) genome build!
--strain <strain_name>
The strain you would like to use as SNP (ALT) genome. Mandatory. For an overview of strain names just run SNPsplit_genome_preparation selecting --list_strains
--list_strains
Displays a list of strain names present in the VCF file for use with --strain <strain_name>
--dual_hybrid
Optional. The resulting genome will no longer relate to the original reference specified with --reference_genome. Instead the new Reference (Ref) is defined by --strain - <strain_name> and the new SNP genome is defined by --strain2 <strain_name>. --dual_hybrid automatically sets --full_sequence.
This will invoke a multi-step process:
1) Read/filter SNPs for first strain (specified with --strain <strain_name>)
2) Write full SNP incorporated (and optionally N-masked) genome sequence for first strain
3) Read/filter SNPs for second strain (specified with --strain2 <strain_name>)
4) Write full SNP incorporated (and optionally N-masked) genome sequence for second strain
5) Generate new Ref/Alt SNP annotations for Strain1/Strain2
6) Set first strain as new reference genome and construct full SNP incorporated (and optionally N-masked) genome sequences for Strain1/Strain2
--strain2 <strain_name>
Optional for constructing dual hybrid genomes (see --dual_hybrid for more information). For an overview of strain names just run SNPsplit_genome_preparation selecting --list_strains
--reference_genome
The path to the reference genome, typically the strain 'Black6' (C57BL/6J), e.g. --reference_genome /scratch/Genomes/Mouse/GRCm39/. Expects one or more FastA files in this folder (file extension: .fa or .fasta)
--skip_filtering
This option skips reading and filtering the VCF file. This assumes that a folder named SNPs_<Strain_Name> exists in the working directory, and that text files with SNP information are contained therein in the following format:
--nmasking
Write out a genome version for the strain specified where Ref bases are replaced with N. In the Ref/SNP example T/G the N-masked genome would now carry an N instead of the T. The N-masked genome is written to a folder called <strain_name>_N-masked/. Default: ON
--full_sequence
Write out a genome version for the strain specified where Ref bases are replaced with the SNP base. In the Ref/SNP example T/G the full sequence genome would now carry a G instead of the T. The full sequence genome is written out to folder called <strain_name>_full_sequence/. May be set in addition to --nmasking. Default: OFF
--no_nmasking
Disable N-masking if it is not desirable. Will automatically set --full_sequence instead
--genome_build [name]
Name of the genome build incorporated into some of the output files. Defaults to 'GRCm39'
--help
Displays this help information and exits
--version
Displays version information and exits