gatk_indelcall.scr

#!/bin/sh
#$ -cwd
#$ -l mem=6G,time=8::

# This step in the pipeline performs indel calling on the input 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 \
 -T IndelGenotyperV2 \
 -R $REF \
 -I $INP \
 -bed $INP.indels.raw.bed \
 -verbose $INP.detailed.output.bed \
 -o $INP.output.vcf

 
#-minCnt 2 \
#-minFraction 0.03 \
#-minConsensusFraction 0.6 \
#-mnr 1000000 
#-O $INP.indels.raw.bed \
#-o $INP.detalied.output.bed \
#-verbose \