BaseRecalibrator as CountCovariates (GATK)

The CountCovariates from GATK](http://www.broadinstitute.org/gatk/) has been replaced by BaseRecalibrator.

The way we can use this new BaseRecalibrator is:

java -Xmx4g -jar GenomeAnalysisTK.jar 
    -l INFO -T BaseRecalibrator 
    -I chr22.marked.realigned.fixed.bam 
    -R GRCh37.73.dna.22.fa 
    -o recalibration_report.grp 
    --knownSites dbsnp_137.hg19.vcf

This call generates the file we will use with PrintReads: recalibration_report.grp

As for CountCovariates, the new BaseRecalibrator needs the dbSNP table in VCF format. This file can be downloaded from the GATK resource bundle, available via FTP:

  • location: `ftp.broadinstitute.org`
  • username: `gsapubftp-anonymous`
  • password:

In the FTP, the dbSNP VCF files (like snp132.vcf< or dbsnp_137.hg19.vcf) are placed in /bundle/2.5/hg19, with their homologous IDX files.

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