can variants be called between two genomes?

Question

[Charles Yin]

Usually, SNP calling is between a reference genome sequence (fasta) and reads (fastq), is it possible to use the commonly used pipeline (BWA alignment and GATK) to call variants between two genomes (fasta files)? For example, I need to find out the SNPs between bacterial strains, which genome sequences have been fully assembled and available. Thank you for your suggestions.

Answer 1

[Lisa Ha]

You could simulate reads from one of the genomes using wgsim and then use a normal pipeline to call the variants. As an alternative, there is a tool called LAST that was built specifically for a genome-genome comparison (I have never used this, though).

Answer 2

[Charles Yin]

Thank you for your solution!