generating a genome reference fasta file
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8 days ago
erl1977 ▴ 60

Hi all,

I have some files (CRAM) that were given to me that are ONT reads aligned to a genome. I would like to generate a 'personal' genome reference for each file. So, essentially, I would like to take the mappings and extract out a consensus fasta sequence for each sample, sort of like generating individual genomes in the pangenome projects. I'm playing around with using "samtools consensus", but not sure if this is the best approach, or if there is another better method out there.

I should mention, that in the output, I would like the new fasta file to incorporate any potential SNPs that may be present in the sample.

(I did try searching for approaches, but haven't been too successful in finding many solutions). Just interested if anyone has done anything similar and has any thoughts.

Thanks for any help.

FASTA BAM reference • 118 views
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