Changes between Version 8 and Version 9 of SOPs/variant_calling_GATK


Ignore:
Timestamp:
06/02/15 17:24:19 (10 years ago)
Author:
thiruvil
Comment:

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  • SOPs/variant_calling_GATK

    v8 v9  
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    565610 - '''Run Base Recalibration''' ([[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_bqsr_BaseRecalibrator.html|BaseRecalibrator]] and [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_PrintReads.html|PrintReads]]) \\
     57Known varians/SNPs in VCF format is required for this step.  If none is available, then use the data itself to "bootstrap" known SNPs, [[http://gatkforums.broadinstitute.org/discussion/44/base-quality-score-recalibration-bqsr | BQSR]]. \\
    5758  * Example 1: java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R human.fasta -I realigned.bam -knownSites dbsnp137.vcf -knownSites gold.standard.indels.vcf -o recal.table
    5859  * Example 2: java -jar GenomeAnalysisTK.jar -T PrintReads -R human.fasta -I realigned.bam -BQSR recal.table -o recal.bam \\