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.
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:
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The first sequence is the reference.
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Make sure the alignment has flat ends, that is, equal length for all sequences.
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Make sure no "-" in the beginning of the alignment, at least for the reference.
./msa2snp.py msa-example.fa > SNPs.txt