Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Why do you have to provide -I and -L if GENOTYPE_GIVEN_ALLELES is used: UnifiedGenotyper

hintzenhintzen Posts: 4Member
edited February 2013 in Ask the team

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: GENOTYPE_GIVEN_ALLELES 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?

Post edited by hintzen on

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