Test-drive the GATK tools and Best Practices pipelines on Terra


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Problem with a BED file and the flag -alleles (HaplotypeCaller)

I'm trying to pass the flag -gt_mode GENOTYPE_GIVEN_ALLELES by giving a list of SNP in a BED file. This BED file has 4 columns (chromosome, initial position, final position, allele, allele). However when trying to pass this file with the -alleles flag I get an error. Allele's argument has a bad value, I need compatible type like BCF2, VCF, VCF3. I tried to transform this BED file into a VCF using an R package (bedr). However, the outcome file does not do the trick. How should I proceed? Do I have another way to obtain a VCF file from my BED to use it in -alleles?

Answers

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