How to extracts variants from multiple sequence alignment files?

Question

[FadyNabil]

I have a clustalw file in .aln format I want to get the variants only from this file

[Pierre Lindenbaum]

see https://github.com/sanger-pathogens/snp_sites / Getting A Vcf File From A Fasta Alignment

[FadyNabil]

I try it but I got this: Alignment sequences.fasta contains sequences of unequal length. Expected length is 712 but got 688 in sequence MT364213.1

[GenoMax]

Did you use Pierre's script or https://github.com/sanger-pathogens/snp-sites ?

[FadyNabil]

I used this link: https://github.com/sanger-pathogens/snp-sites

[GenoMax]

That link requires an aligned fasta format file which is not the same as .aln file you have. I suggest you use Pierre's script in this answer: Getting A Vcf File From A Fasta Alignment

[FadyNabil]

I found that the sequences must have the same length

[Joe]

If your sequences aren't the same length, they aren't aligned, so you need to check your input data properly.