Recalibration

= Recalibration = Walking through the BAM file and rewrite the quality scores. Make a temp directory mkdir -p ${tmp_folder}_recal

Running GATK recalibration java -Xmx${heap}m -Djava.io.tmpdir\=${tmp_folder}_recal \ -jar $gatk \ -l INFO \ -R $REF \ -I $PWDS/${subjectID}.realigned.srt.bam \ -T TableRecalibration \ --default_platform Illumina \ --default_read_group MP1 \ --out $PWDS/${subjectID}.realigned.recal.bam \ -recalFile $PWDS/${subjectID}.flt.recal_v1.csv \ -L $ExonFile

Indexing $samtools index $PWDS/${subjectID}.realigned.recal.bam

Remove the temp directory rmdir -p ${tmp_folder}_recal

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