The code in this repository was used to find putative introgressions in modern tomato genomes. This work is a part of a larger panSV-genome analysis. The code is written expressly for that analysis, and will not be updated or maintained for future use.
- python3
- numpy (developed, and run on v1.17.2)
There is no installation required. Just run python3 get_distances.py to see the following usage message.
usage: get_distances.py [-h] [-m 5]
<SVs.vcf> <chr_name> <group.txt> <SP>
<reference.fasta.fai> <100000>
Get Jaccard similarity between SLL and a comparison group.
positional arguments:
<SVs.vcf> SV vcf file with support vectors. Only one chromosome
at a time allowed.
<chr_name> Name of reference chromosome.
<group.txt> First column is the phylogenetic group (SLC, SP, GAL,
CHE, or SLL), second column is the accession
<SP> Group to compare to SLL (SLC, SP, GAL, or CHE)
<reference.fasta.fai>
Fasta index file for the reference genome
<100000> Introgression window size.
optional arguments:
-h, --help show this help message and exit
-m 5 minimum number of SVs needed to calculate Jaccard