How to do a pairwise alignment and convert the result to a VCF file?
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4 months ago
arturo.marin ▴ 10

Hi,

I need to do a lot of pairwise alignments and obtain a VCF file of each alignment. The purpose of this is to find the mutations between different ORFs of a reference genome and this ORFs in other genomes (one by one). Is there some combination of software that can do this? I am not sure that this can be done with MAFFT or muscle, since they are multiple aligner, and I am not sure that this can be done with a mapper like minimap2 or BWA, since mappers works with reads.

Maybe I could use MAFFT and build a parser in Python to see the mutations in each alignment, but maybe there is a program (or combination of program) that does this more easily.

Thanks,

VCF Genomics mutations • 200 views
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Entering edit mode
4 months ago

You could use minimap2 and paftools, some inspiration can be found here: https://github.com/lh3/CHM-eval/blob/master/dip-call/README.md

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