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.
Why do you have to provide -I and -L if GENOTYPE_GIVEN_ALLELES is used: UnifiedGenotyper
Previously I have been running a command like this:
java -jar /path/GenomeAnalysisTK.jar \ -T UnifiedGenotyper \ -R /path/human_g1k_v37.fasta \ -et NO_ET \ -K /path/key \ -out_mode EMIT_ALL_SITES \ --input_file /path/bam \ -L /path/intervals \ -gt_mode GENOTYPE_GIVEN_ALLELES \ --alleles /path/vcf \ --dbsnp /path/dbsnp_135.b37.vcf \ -o /path/my.vcf
But I was reading the documentation again and I read this statement:
only the alleles passed in from a VCF rod bound to the -alleles argument will be used for genotyping
Which lead me to believe that there wasn't a need to include the lines:
--input_file /path/bam \
-L /path/intervals \
because it would be redundant. But when I try to run without those line I get back an error message:
Walker requires reads but none were provided.
Can you give an explaination as to why both of those lines AND GENOTYPE_GIVEN_ALLELES would be needed?