Entering edit mode
8.0 years ago
outlier95
▴
30
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?