A question about reference genome for creating the consensus sequence

Question

[me]

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

Answer 1

[ATpoint]

It is the consensus for all reads that overlap a given base, it's not a genome consensus unless your reads cover the entire genome.

[me]

Hi, yes, my cram files cover the whole genome, which is actually individual genome information. I wonder how to adjust the base genome. Thanks.

[ATpoint]

You aligned your data, that is your reference genome to compare against. If you want to change reference then realign.

[me]

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.

[GenoMax]

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