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

hintzenhintzen Member Posts: 4
edited February 2013 in Ask the GATK 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 \


  --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?

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,690 admin

    @hintzen, what exactly do you want the program to genotype if not sequence reads?

    Geraldine Van der Auwera, PhD

  • hintzenhintzen Member Posts: 4

    @Geraldine_VdAuwera I am not sure I understand. I want to sequence reads but doesn't giving GENOTYPE_GIVEN_ALLELES do the same job as -I -L ?

  • jlrfloresjlrflores Member Posts: 31

    If I want to genotype given alleles and only look at the sites in the given vcf, do I need to provide mysites.vcf to both the --alleles and -L parameters?

  • tommycarstensentommycarstensen United KingdomMember Posts: 400 ✭✭✭

    @jlrflores You don't have to, but I think it will be faster, because it doesn't traverse all reads of your bam. Does that make sense?

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