Create reference genome from my WGS data (custom reference)


May I ask a question to create the reference from my own WGS data using Galaxy. I have my WGS data that was already mapped with the native reference (BAM file). Then I want to use this kind of data as a reference for further analysis with another dataset to identify SNPs. Previously, I try to create it by converting the BAM file to BED and then using Bedtools: getfastabed to generate the FASTA file. However, this FASTA seems not the reference from my own data. Could you recommend the step to generate the FASTA file for reference? I try to file the protocol in Custom Reference Genome topic, but there is no mention about the way to generate the FASTA file from the individual data. Only the FASTA format is mentioned.



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