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Old 10-09-2013, 03:40 AM   #16
Location: Milan

Join Date: May 2013
Posts: 40

@choishingwan ,

Thanks for your prompt reply. I would like to tell you that I am using the version 2.3 not the 2.7 one so is it wrong to use the DBSNP_137.vcf file with that? I hope this should not be a problem for the GATK toolkit to work with the latest DBSNP file right as this is just the upated data set also in a step I see you have used the print reads command and it is usually done when you merge all you samples together for and generate a single bam file and then try to call the SNP and INDEL but since am just developing a new pipeline with a test sample from the 1000 G project I have only one sample ( paired-end) where am trying to understand each step of the pipeline and so that once I have my samples I can use that pipeline on them. Please can you clarify the the doubts about the print reads step or can I use the below script when am not merging all the samples together and use Table Recalibrator

ava -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
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