To call variants can I use my aligned WGS data as a reference genome

Question

[mls]

Hi,

I have several yeast WGS data for different time data points. I wanna call variants depending on the first time point WGS data(I already map my samples with bowtie). But I could not figure out how to use my first time point WGS data as a reference rather than S288C fasta. I would be glad if someone can give me some ideas.

Thank you

[Pierre Lindenbaum]

the bam are mapped on S288C fasta isn't it ? why would you need another reference ?

[mls]

Yes they are but I wanna compare one of my samples with others , rather S288C.

[GenoMax]

Then create an alternate Reference with data for the sample: https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker