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Old 10-09-2013, 02:59 AM   #12
vd4mindia
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Location: Milan

Join Date: May 2013
Posts: 40
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@thedamian,

Yes I fixed it , I indexed it again and then made the call and the local realignment step is running now. But i need some inputs for the base quality recalibration step. In the above thread this step is written as below
java -Xmx5g -jar GenomeAnalysisTK.jar -nt 4 -T CountCovariates -l INFO -R hg19.fa -I realigned.bam -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile recalFile -knownSites dbsnp_135.hg19.vcf

Since during my Realigner Target Creator step I used dbSNP_137.vcf for known sites I should be using the same as well for the Base quality step right?

java -Xmx14g -jar /data/PGP/gmelloni/GenomeAnalysisTK-2.3-4-g57ea19f/GenomeAnalysisTK.jar -R /scratch/GT/vdas/test_exome/exome/hg19.fa -I SRR062634_marked.sorted.bam -T RealignerTargetCreator -known /scratch/GT/vdas/test_exome/exome/databases/dbsnp_137.hg19.vcf -known /scratch/GT/vdas/test_exome/exome/databases/1000G_phase1.indels.hg19.vcf -known /scratch/GT/vdas/test_exome/exome/databases/Mills_and_1000G_gold_standard.indels.hg19.vcf -o SRR062634_marked.sorted.bam.inervals -S LENIENT

As you can see the known sites /scratch/GT/vdas/test_exome/exome/databases/dbsnp_137.hg19.vcf

So my script for this step should be

For the Base calibrator( i see some place its written count covariates, which should I do) any suggestion but am following base calibrator below is the command

java -Xmx14g -jar /data/PGP/gmelloni/GenomeAnalysisTK-2.3-4-g57ea19f/GenomeAnalysisTK.jar -nt 8 -T BaseRecalibrator -R /scratch/GT/vdas/test_exome/exome/hg19.fa -knownSites /scratch/GT/vdas/test_exome/exome/databases/dbsnp_137.hg19.vcf -I SRR062634.realigned.bam -o SRR062634.realigned.recal.csv -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate -S LENIENT

for table recalibration

java -Xmx14g -jar /data/PGP/gmelloni/GenomeAnalysisTK-2.3-4-g57ea19f/GenomeAnalysisTK.jar -T TableRecalibration -R /scratch/GT/vdas/test_exome/exome/hg19.fa -I SRR062634.realigned.bam -o SRR062634.realigned.bam.recal.bam -BQSR SRR062634.realigned.recal.csv -S LENIENT

Please let me know if this looks correct or not?
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