This project contains a number of PERL scripts for converting VCF files to an alignment of SNPs. This is a subproject of the larger core phylogenomics pipeline project located at https://github.com/apetkau/core-phylogenomics.
Following the install guide of the parent project should automatically download this software. However, if you wish to install this project independently please follow the below steps.
Download the software with:
$ git clone https://github.com/apetkau/vcf2pseudoalignment.git
This project requires vcftools as a dependency. Please download and install this software.
In addition, this software requires the Perl modules from vcftools someplace within your library path (in PERL5LIB for example). This can be accomplished by running, for example:
$ export PERL5LIB=/path/to/vcftools/lib/perl5/site_perl/:$PERL5LIB
Or, you can simply link up the appropriate perl modules within the vcf2pseudoalign/lib directory. For example:
$ ln -s /path/to/vcftools/lib/perl5/site_perl/*.pm /path/to/vcf2pseudoalign/lib
$ ls /path/to/vcf2pseudoalign/lib
Align CorePositions.pm FaSlice.pm InvalidPositions.pm NucmerPositionsChecker.pm PositionsTable.pm Vcf.pm VcfStats.pm
In order to run the tests, please run the command:
$ cd /path/to/vcf2pseudoalign
$ prove
t/compare_pseudoalign_nucmer.t .. ok
t/extract_snps_metaalign.t ...... ok
t/find-positions-used.t ......... ok
t/nucmer_align.t ................ ok
t/variant_calls.t ............... ok
t/vcf2core.t .................... ok
All tests successful.
Files=6, Tests=232, 41 wallclock secs ( 0.28 usr 0.02 sys + 30.71 cusr 7.60 csys = 38.61 CPU)
Result: PASS