msa2snp

SNP and indel calls from multiple sequence alignment (MSA)

I need to call SNPs in a multiple sequence alignment from several sanger sequencing sequences, but did not find a simple software that can do that, so I just wrote one.

After you get the SNPs and their locations, then you can use another script mysnpeffv2.py to check SNP effects.

Input

The only input is a MSA file in fasta format. You can prepare the alignment in many software, such as MEGA and Aliview. Then just save them in fasta format. Some format requirement:

1. The first sequence is the reference.

2. Make sure the alignment has flat ends, that is, equal length for all sequences.

3. Make sure no "-" in the beginning of the alignment.

Usage

# to create only a snp table with A T G C alleles
python msa2snp.py msa-example.fa > SNPs.txt

# to create vcf format output (this will also create a file "snptable.txt" for a snp table as above)
python msa2vcf.py msa-example.fa > snp.vcf

Update

• 2022-11-11: add msa2vcf.py to create vcf format output