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# Getting very less entries in vcf file??

Member Posts: 13

Dear Developers,

I Run Unified genotyper for identify the indels and deletion.
I used Realigner target creater got forIndelRealigner.intervals. used this output for Indel Realigner and get the output bam file which i gave as input toUnified Genotyper.
I got result as

# CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BRCA1

But if i run without these steps (Realigner target creater, Indel Realigner) i am getting the same output.
Also i used the same dataset and run it in samtools and got more SNP.

I am looking for a deletion in the dataset.
I would like to get the result from GATK Could you please suggest on the same.

Thanks
Sridhar

Tagged:

• Member Posts: 13

Hello Geraldine,

Thank you for the detailed reply.
Actually in the analysis we tried with a software(not samtools) for variant calling and compared the results with GATK here we dint get the deletion we observed.
I tried Haplotypecaller earlier i got few entries more but the deletion which i expect i dint get it..

Thanks
Sridhar

I see -- you should definitely try the genotype given alleles mode, then. That will at least give you some metrics on what the caller thinks of the deletion you observe.

Geraldine Van der Auwera, PhD

• Member Posts: 13

Hello Geraldine,

Cold you please tell me how to use the option GENOTYPE_GIVEN_ALLELES ??
Because it shows error wehn i use UnifiedGenotyper and haplotypecaller..

Thanks
Sridhar

Can you tell me what command line you tried and what error you got?

Geraldine Van der Auwera, PhD

• Member Posts: 13

java -jar galaxy/apps/GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -R brca.fasta -T UnifiedGenotyper -I BRCA_S21_picard.bam --GENOTYPE_GIVEN_ALLELES

Oh, I see. You need to provide a VCF file containing the alleles you are looking for, with the --alleles argument as described here. You can also provide the same VCF to the -L` argument if you want to restrict your analysis to just those sites, but that is optional.