Substituting heterozygous sites by randomly sampling one allele
For those familiar with GATK, FastaAlternateReferenceMaker (unless the --useIUPAC flag is added) always uses the alternate allele at heterozygous SNP sites. I would like to "haploidize" sampled loci by randomly sampling one allele at heterozygous sites. Is there a tool that can do this, provided a reference sequence and sample-specific vcf file?
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outlier95 •
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