Getting very less entries in vcf file??

sridhar28sridhar28 Posts: 13Member

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

gi|262359905|ref|NG_005905.2| 48155 . G A 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.466;DP=47;Dels=0.00;FS=2.721;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.31;MQ0=0;MQRankSum=-4.812;QD=8.25;ReadPosRankSum=0.535 GT:AD:DP:GQ:PL 0/1:25,22:45:99:416,0,676

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

Best Answer

Answers

  • sridhar28sridhar28 Posts: 13Member

    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

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,804Administrator, GATK Developer admin

    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

  • sridhar28sridhar28 Posts: 13Member

    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

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,804Administrator, GATK Developer admin

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

    Geraldine Van der Auwera, PhD

  • sridhar28sridhar28 Posts: 13Member

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

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,804Administrator, GATK Developer admin

    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.

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.