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This should work if you know your sequences are related, otherwise is safer to compute local alignments with BLAST
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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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This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
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Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
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