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  • GATK recalibration confused, one step or two step?

    Just based my reading
    Previously, it was:
    Quote:
    java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R hg19.fa --DBSNP dbsnp132.txt -I input.marked.realigned.fixed.bam -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile input.recal_data.csv

    java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R hg19.fa -I input.marked.realigned.fixed.bam -T TableRecalibration --out input.marked.realigned.fixed.recal.bam -recalFile input.recal_data.csv

    Then some suggested (http://seqanswers.com/forums/showthr...14038&page=5):
    Quote:
    java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R hg19.fa -knowSites dbsnp132.txt -I input.marked.realigned.fixed.bam -T BaseRecalibrator -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate --out input.recal_data.csv

    From GATK doc:
    java -Xmx4g -jar GenomeAnalysisTK.jar \
    -T BaseRecalibrator \
    -I my_reads.bam \
    -R resources/Homo_sapiens_assembly18.fasta \
    -knownSites bundle/hg18/dbsnp_132.hg18.vcf \
    -knownSites another/optional/setOfSitesToMask.vcf \
    -o recal_data.grp
    with this additional step only if using several bam files (if I understand well the documentation: "PrintReads can dynamically merge the contents of multiple input BAM files, resulting in merged output sorted in coordinate order" )
    Quote:
    java -Xmx2g -jar GenomeAnalysisTK.jar \
    -R ref.fasta \
    -T PrintReads \
    -o output.bam \
    -I input1.bam \
    -I input2.bam \
    --read_filter MappingQualityZero

    What should I do?

  • #2
    Anyway, here is what I did:

    java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R hg19.fa -knownSites 00-All.vcf -I input.nodup.realigned.fixed.bam -T BaseRecalibrator -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate --out input.csv

    Will run the print read now

    Comment


    • #3
      Hi there,

      These tools have evolved slightly over the past few months, so make sure to read the latest documentation here: http://www.broadinstitute.org/gatk/guide/best-practices

      Also, look at the presentations from the latest GATK workshop here:

      Comment

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