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Is there a conflict between EMIT_ALL_CONFIDENT_SITES and GENOTYPE_GIVEN_ALLELES
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 \
-out_mode EMIT_ALL_CONFIDENT_SITES \
-l INFO \
-A HaplotypeScore \
-A InbreedingCoeff \
-glm SNP \
-nt 1 \
Am I correct?