Hi, I wonder how the samtools consensus work without explicitly pointing out the reference genome. If I intend to add a reference genome to generate the consensus sequence, is it possible based on samtools? Thanks a lot.
Reference: https://www.htslib.org/doc/samtools-consensus.html
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Hi, thanks for your information. I am a bit confused now. Does this mean the cram file already contained reference genome information? I intend to generate a new fasta file based on the cram file, so that means I only need to consider the consensu sequence. Is it correct? Thanks.
I wonder how to adjust the base genome.
If you are looking to make changes to the reference you used for alignment then look into https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker
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