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

Posts: 4
edited February 2013

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?

Tagged:

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

Geraldine Van der Auwera, PhD

• 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 ?

• Posts: 32

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?

• United KingdomPosts: 404 ✭✭✭

@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?