Changes between Version 5 and Version 6 of SOPs/variant_calling_GATK


Ignore:
Timestamp:
01/16/14 15:58:36 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/variant_calling_GATK

    v5 v6  
    5656and then make plots of how they've changed (which requires the R [[http://cran.r-project.org/web/packages/gsalib/index.html|'gsalib']] R package).
    5757  * Example 4: java -jar GenomeAnalysisTK.jar -T AnalyzeCovariates -R human.fasta -before recal.table -after after_recal.table -plots recal_plots.pdf
     58All applied to our sample data:
     59  * bsub java -jar /usr/local/gatk/GenomeAnalysisTK.jar -T BaseRecalibrator -I Reads_1.bwa.dedup.realigned.bam -R /path/to/genome/genome.fa -o Reads_1.bwa.recal_data.txt -knownSites SNPs_from_NCBI.sorted.vcf
     60  * bsub java -jar /usr/local/gatk/GenomeAnalysisTK.jar -T PrintReads -I Reads_1.bwa.dedup.realigned.bam -R /path/to/genome/genome.fa -BQSR Reads_1.bwa.recal_data.txt -o Reads_1.bwa.dedup.realigned.recal.bam
     61  * bsub java -jar /usr/local/gatk/GenomeAnalysisTK.jar -T BaseRecalibrator -I Reads_1.bwa.dedup.realigned.bam -R /path/to/genome/genome.fa -knownSites SNPs_from_NCBI.sorted.vcf -BQSR Reads_1.bwa.recal_data.txt -o Reads_1.bwa.after_recal.txt
     62  * bsub java -jar /usr/local/gatk/GenomeAnalysisTK.jar -T AnalyzeCovariates -R /path/to/genome/genome.fa -before Reads_1.bwa.recal_data.txt -after Reads_1.bwa.after_recal.txt -plots Reads_1.bwa.recal_plots.pdf
     63
    5864\\
    5965'''Compress BAM with [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_compression_reducereads_ReduceReads.html|ReduceReads]]''' [Optional] \\