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A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
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After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1])
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Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome.
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