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RNAseq Library to SNP Call using GATK

YogeshYogesh south koreaMember

Hi ,

I am working on SNP detection on multiple pair end RNAseq library:

after indel realignment, I want perform base quality score recalibration by using these two steps, I do not have any information about known SNP,INDEL.VCF. If I do not provide this option is it ok?

java -jar GenomeAnalysisTK.jar \
-T BaseRecalibrator \
-R refgenome.fasta\
-knownSites known_snps_indels.vcf \
-I sample1.sorted.dedup.realigned.fixmate.bam \
-o sample1.sorted.dedup.realigned.fixmate.recal_data.table \
-cov ReadGroupCovariate \
-cov QualityScoreCovariate \
-cov CycleCovariate

java -jar GenomeAnalysisTK.jar \
-T PrintReads \
-R refgenome.fasta \
-BQSR sample1.sorted.dedup.realigned.fixmate.recal_data.table \
-I sample1.sorted.dedup.realigned.fixmate.bam \
-o sample1.sorted.dedup.realigned.fixmate.recal.bam

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