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senguptadsenguptad SingaporeMember

I am using multiple RNA seq samples from same individual and genotyping for dbsnp locations. I need to get all 0/0 0/1 and 1/1 in my matrix for all samples whichever have reasonable coverage.

Emitting all confident sites force the program looking at every possible site across all samples and also get 0/0 annotation while using unified genotyper. On the other hand since I want to just genotype DBSNPs is it fine to activate genotype given allele? Will I still get 0/0

It should the look like

java -Xmx4g -jar /mnt/projects/senguptad/ctc/K562-allele/GenomeAnalysisTK.jar \
-T UnifiedGenotyper \
-R /mnt/projects/senguptad/ctc/hg19/hg19.fa \
--dbsnp /mnt/AnalysisPool/libraries/genomes/hg19/dbsnp/dbsnp_137.hg19.vcf \
-I /mnt/projects/senguptad/ctc/GLIO/GLIO/unique/newresult4/ready_readgrp_SRR1294973.bam \
-I /mnt/projects/senguptad/ctc/GLIO/GLIO/unique/newresult4/ready_readgrp_SRR1294974.bam \
--out /mnt/projects/senguptad/ctc/GLIO/GLIO/unique/newresult4/finalX.vcf \
-stand_call_conf 30.0 \
-stand_emit_conf 10.0 \
--alleles /mnt/AnalysisPool/libraries/genomes/hg19/dbsnp/dbsnp_137.hg19.vcf
-l INFO \
-A HaplotypeScore \
-A InbreedingCoeff \
-glm SNP \
-nt 1 \

Am I correct?



  • SheilaSheila Broad InstituteMember, Broadie admin


    Yes, there is a conflict between the two. Genotype_Given_Alleles mode takes precedence if you input both, so you will not get the 0/0 sites.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I would recommend running with EMIT_ALL_CONFIDENT_SITES and specifying dbsnp as the -L (intervals) of interest.

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    @Geraldine_VdAuwera said:
    I would recommend running with EMIT_ALL_CONFIDENT_SITES and specifying dbsnp as the -L (intervals) of interest.

    @senguptad I would go full throttle blind folded and use -gt_mode GENOTYPE_GIVEN_ALLELES and --alleles with --output_mode EMIT_ALL_SITES. I would definitely use --intervals to avoid reading the entire bam file as suggested by Geraldine. I can't remember, if it's also necessary to use -stand_call_conf 0 and -stand_emit_conf 0 to emit all sites. Since I suggested you go blind folded you cannot check... But EMIT_ALL_SITES should output your monomorphic homREF sites, which is what you asked for. Good luck!

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