Question: Substituting heterozygous sites by randomly sampling one allele
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gravatar for outlier95
3.4 years ago by
outlier9510
outlier9510 wrote:

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?

fasta snp gatk vcf • 681 views
ADD COMMENTlink written 3.4 years ago by outlier9510
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