Changes between Version 9 and Version 10 of SOPs/variant_calling_GATK
- Timestamp:
- 06/02/15 17:24:53 (10 years ago)
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SOPs/variant_calling_GATK
v9 v10 55 55 \\ 56 56 10 - '''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]]) \\ 57 Known varian s/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]]. \\57 Known variants/SNPs in VCF format is required for this step. If none is available, then use the data itself to "bootstrap" known SNPs, see [[http://gatkforums.broadinstitute.org/discussion/44/base-quality-score-recalibration-bqsr | BQSR]]. \\ 58 58 * 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 59 59 * Example 2: java -jar GenomeAnalysisTK.jar -T PrintReads -R human.fasta -I realigned.bam -BQSR recal.table -o recal.bam \\