gatk_recalibrate.scr

#!/bin/sh
#$ -cwd
# -l mem=8G,time=8::

# This step in the pipeline performs recalibration of the bam file.

GLOBAL="global_config.sh"

if [[ -e $GLOBAL ]]
then
        . $GLOBAL
else
        echo "Global config file not found. Exiting."
        exit 1
fi

USAGE="Usage: $0 -I <Input bam file> -R <Reference fasta> -L \"#:#-#\"]"

while getopts I:L:R:h o
do      case "$o" in
        I)      INP="$OPTARG";;
        L)      CHR="$OPTARG";;
        R)      REF="$OPTARG";;
        h)      echo $USAGE
                exit 1;;
        esac
done

if [[ $INP == "" || $REF == ""  ]]
then
        echo $USAGE
        exit 1
fi

CHR_NAME=`$SAMTOOLS idxstats $INP | grep chr`

if [[ $CHR != "" ]]
then
        if [[ `grep chr $CHR` == "" && -n $CHR_NAME ]]
        then
                CHR="chr${CHR}"
        fi
fi

$GATK \
 -L $CHR \
 -R $REF \
 -T TableRecalibration \
 -I $INP \
 -recalFile $INP.recal_data.csv \
 --out $INP.recalibrated.bam

if [[ $? != 0 || `grep "$ERRORMESSAGE" recalibrate.output pipeline.output` != "" ]]
then
        echo "Recalibration FAILED"
        exit 1
fi

rm -f $INP $INP.bai

$SAMTOOLS index $INP.recalibrated.bam

if [[ $? != 0 ]]
then
        echo "Recalibration: Samtools indexing FAILED"
        exit 1
fi

echo "$0: samtools index complete"