Question: Mouse Dbsnp Database For Quality Score Recalibration From Gatk
gravatar for Tonyzeng
5.2 years ago by
Tonyzeng300 wrote:

Does anybody know where to download mouse dbsnp database for quality score recalibration from GATK (commands are as below but using human dbsnp132.txt.

Thank you!

$java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R genome.fa --DBSNP dbsnp132.txt -I K1.marked.realigned.fixed.bam -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile k1.recal_data.csv

gatk dbsnp mouse • 1.7k views
ADD COMMENTlink written 5.2 years ago by Tonyzeng300

sorry I just found that latest version for the GATL(2.7) does not use CountCovariates but use BaseRecalibrator, the commands in my post does not work anymore.

ADD REPLYlink written 5.2 years ago by Tonyzeng300
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