Hi All
I have a quick question about calling SNP/InDel from a whole genome alignment file which is in FASTA format. I have aligned 45 assembled bacterial genomes (~4Mb each) using Mugsy tool and converted the MAF output to FASTA. One of the 45 genomes is the reference. Now I want a table (preferably in VCF format) showing SNP/InDels in 44 strains as compared to my reference strain. Please suggest how to do this?
Thanks
baika
I have a quick question about calling SNP/InDel from a whole genome alignment file which is in FASTA format. I have aligned 45 assembled bacterial genomes (~4Mb each) using Mugsy tool and converted the MAF output to FASTA. One of the 45 genomes is the reference. Now I want a table (preferably in VCF format) showing SNP/InDels in 44 strains as compared to my reference strain. Please suggest how to do this?
Thanks
baika
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