To call variants can I use my aligned WGS data as a reference genome
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13 months ago
mls • 0

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

VCF samtools reference-genome • 580 views
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the bam are mapped on S288C fasta isn't it ? why would you need another reference ?

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

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

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