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Old 05-31-2016, 01:16 PM   #1
Location: Binghamton, NY

Join Date: Jan 2013
Posts: 13
Default Building vcf of known variants for GATK Haplotype Caller with GENOTYPE_GIVEN_ALLELES

I have reads from a pool of recombinants between two parental genomes.

As such, I am only interested in calling variants for the known set of variable alleles between the two parental genomes.

The GATK haplotype caller allows for this with the argument GENOTYPE_GIVEN_ALLELES and by providing the -alleles argument with a vcf file with the variable sites and alleles of interest.

However, I have been unable to find any type of guide anywhere for the preparation of this file and I have limited experience working with vcf files.

Ideally, I would like to generate this file directly from an alignment of these two genomes, but my normal workflow involving multiple sequence alignment does not output a vcf file.

Does anyone have any tips on a good workflow for generating the file for this purpose?
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