Can BWA align genome fasta to fasta?

Question

[kgwkk2]

I want to compare same species, different strain genomes by making each genome's VCF file. And type strain was used for standard genome for reference(https://www.ncbi.nlm.nih.gov/assembly/GCF_014117465.1). In case of illumina short read sequences (raw data, fastq), I could align short reads based on reference genome, and make BAM file for VCF file making

So I want to align genome fasta to another reference genome fasta for comparing and making VCF file. Does BWA or other aligner program can do this job? Or is it the only way to find SRA of the genome

Answer 1

[Istvan Albert]

You can align entire smaller genomes with minimap2 - you won't be able to call snps with a typical SNP caller though, as most of these tools require multiple measurements per base and what you have is a single one.

In general, note that the BAM and VCF formats were designed to represent many short reads and ill suited for representing pairwise, whole genome alignments.

By the way, I have been exploring this issue of turning pariwise alignments to VCF myself, within my bio package and I wrote an alignment reformatter that can turn aligned FASTA files (such as the ones produced via MAFFT) into VCFs.

1. align with MAFFT
2. reformat resulting alignment as VCF

https://www.bioinfo.help/bio-format.html

But I will say the whole software is exploratory and never been used heavily, probably has bugs and inconsistencies.

In your case thought, you should look for tools written for this specific purpose:

https://github.com/marbl/parsnp