Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?