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ebCall_v2.sh
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#!/bin/bash
write_usage() {
echo ""
echo "Usage: `basename $0` <path to the target tumor bam file> <path to the target normal bam file> <path to the output directory> <path to the text file of the list for normal reference samples> [<path to the config.sh>]"
echo ""
}
INPUTBAM_TUM=$1
INPUTBAM_NOR=$2
OUTPUTPATH=$3
REFERENCELIST=$4
config=$5
readonly DIR=`dirname ${0}`
if [ $# -le 3 -o $# -ge 6 ]; then
echo "wrong number of arguments"
write_usage
exit 1
fi
if [ $# -eq 4 ]; then
config=${DIR}/config.sh
fi
if [ $# -eq 5 ]; then
if [ ! -f ${config} ]; then
echo "${config} dose not exists"
write_usage
exit 1
fi
fi
conf_dir=`dirname ${config}`
conf_dir=`echo $(cd ${conf_dir} && pwd)`
source ${conf_dir}/${config}
source ${DIR}/utility.sh
if [ -f ${conf_dir}/${config} ]; then
echo "${conf_dir}/${config} exists."
else
echo "${conf_dir}/${config} does not exists."
fi
check_file_exists ${INPUTBAM_TUM}
check_file_exists ${INPUTBAM_NOR}
check_file_exists ${REFERENCELIST}
targetfile=${REFERENCELIST}
cat $targetfile | while read line; do
if [ ! -f $line ]; then
echo "$line does not exists."
echo "Please check $targetfile"
exit 1
fi
done
if [ $? -ne 0 ]; then
exit 1
fi
check_file_exists ${PATH_TO_REF}
check_mkdir ${OUTPUTPATH}/tmp
# exec > >(tee ${OUTPUTPATH}/tmp/command.log)
# pileup the tumor bam file
##########
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "${PATH_TO_SAMTOOLS}/samtools mpileup -BQ0 -d10000000 -f ${PATH_TO_REF} -q ${TH_MAPPING_QUAL} ${INPUTBAM_TUM} > ${OUTPUTPATH}/tmp/temp.tumor.pileup"
${PATH_TO_SAMTOOLS}/samtools mpileup -BQ0 -d10000000 -f ${PATH_TO_REF} -q ${TH_MAPPING_QUAL} ${INPUTBAM_TUM} > ${OUTPUTPATH}/tmp/temp.tumor.pileup
check_error $?
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "${PATH_TO_SAMTOOLS}/samtools mpileup -BQ0 -d10000000 -f ${PATH_TO_REF} -q ${TH_MAPPING_QUAL} ${INPUTBAM_NOR} > ${OUTPUTPATH}/tmp/temp.normal.pileup"
${PATH_TO_SAMTOOLS}/samtools mpileup -BQ0 -d10000000 -f ${PATH_TO_REF} -q ${TH_MAPPING_QUAL} ${INPUTBAM_NOR} > ${OUTPUTPATH}/tmp/temp.normal.pileup
check_error $?
##########
# make count files for mismatches, insertions and deletions
# mismatch count is performed considering bases whose quality is more than ${TH_BASE_QUAL}.
##########
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "${DIR}/subscript/Pileup2Base.o ${TH_BASE_QUAL} ${MIN_TUMOR_DEPTH} ${OUTPUTPATH}/tmp/temp.tumor.pileup ${OUTPUTPATH}/tmp/temp.tumor.base ${OUTPUTPATH}/tmp/temp.tumor.ins ${OUTPUTPATH}/tmp/temp.tumor.del ${OUTPUTPATH}/tmp/temp.tumor.depth"
${DIR}/subscript/Pileup2Base.o ${TH_BASE_QUAL} ${MIN_TUMOR_DEPTH} ${OUTPUTPATH}/tmp/temp.tumor.pileup ${OUTPUTPATH}/tmp/temp.tumor.base ${OUTPUTPATH}/tmp/temp.tumor.ins ${OUTPUTPATH}/tmp/temp.tumor.del ${OUTPUTPATH}/tmp/temp.tumor.depth
check_error $?
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "${DIR}/subscript/Pileup2Base.o ${TH_BASE_QUAL} ${MIN_NORMAL_DEPTH} ${OUTPUTPATH}/tmp/temp.normal.pileup ${OUTPUTPATH}/tmp/temp.normal.base ${OUTPUTPATH}/tmp/temp.normal.ins ${OUTPUTPATH}/tmp/temp.normal.del ${OUTPUTPATH}/tmp/temp.normal.depth"
${DIR}/subscript/Pileup2Base.o ${TH_BASE_QUAL} ${MIN_NORMAL_DEPTH} ${OUTPUTPATH}/tmp/temp.normal.pileup ${OUTPUTPATH}/tmp/temp.normal.base ${OUTPUTPATH}/tmp/temp.normal.ins ${OUTPUTPATH}/tmp/temp.normal.del ${OUTPUTPATH}/tmp/temp.normal.depth
check_error $?
# extract putative germline mutations
##########
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "perl ${DIR}/subscript/filterBase.barcode.pl ${OUTPUTPATH}/tmp/temp.normal.base ${MIN_NORMAL_DEPTH} > ${OUTPUTPATH}/tmp/temp.normal.base.filt"
perl ${DIR}/subscript/filterBase.barcode.pl ${OUTPUTPATH}/tmp/temp.normal.base ${MIN_NORMAL_DEPTH} > ${OUTPUTPATH}/tmp/temp.normal.base.filt
check_error $?
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "perl ${DIR}/subscript/filterBase_del.barcode.pl ${OUTPUTPATH}/tmp/temp.normal.del ${MIN_NORMAL_DEPTH} > ${OUTPUTPATH}/tmp/temp.normal.del.filt"
perl ${DIR}/subscript/filterBase_del.barcode.pl ${OUTPUTPATH}/tmp/temp.normal.del ${MIN_NORMAL_DEPTH} > ${OUTPUTPATH}/tmp/temp.normal.del.filt
check_error $?
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "perl ${DIR}/subscript/filterBase_ins.barcode.pl ${OUTPUTPATH}/tmp/temp.normal.ins ${MIN_NORMAL_DEPTH} > ${OUTPUTPATH}/tmp/temp.normal.ins.filt"
perl ${DIR}/subscript/filterBase_ins.barcode.pl ${OUTPUTPATH}/tmp/temp.normal.ins ${MIN_NORMAL_DEPTH} > ${OUTPUTPATH}/tmp/temp.normal.ins.filt
check_error $?
# filter candidate of variation between tumor and normal
##########
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "${PATH_TO_SAMTOOLS}/samtools view -H ${INPUTBAM_TUM} > ${OUTPUTPATH}/tmp/sam.header"
${PATH_TO_SAMTOOLS}/samtools view -H ${INPUTBAM_TUM} > ${OUTPUTPATH}/tmp/sam.header
check_error $?
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "${DIR}/subscript/CompBase.o ${OUTPUTPATH}/tmp/temp.tumor.base ${OUTPUTPATH}/tmp/temp.normal.base ${MIN_TUMOR_DEPTH} ${MIN_NORMAL_DEPTH} ${MIN_TUMOR_VARIANT_READ} ${MIN_TUMOR_ALLELE_FREQ} ${MAX_NORMAL_ALLELE_FREQ} ${OUTPUTPATH}/tmp/sam.header > ${OUTPUTPATH}/tmp/temp.tumor_normal.base.filt"
${DIR}/subscript/CompBase.o ${OUTPUTPATH}/tmp/temp.tumor.base ${OUTPUTPATH}/tmp/temp.normal.base ${MIN_TUMOR_DEPTH} ${MIN_NORMAL_DEPTH} ${MIN_TUMOR_VARIANT_READ} ${MIN_TUMOR_ALLELE_FREQ} ${MAX_NORMAL_ALLELE_FREQ} ${OUTPUTPATH}/tmp/sam.header > ${OUTPUTPATH}/tmp/temp.tumor_normal.base.filt
check_error $?
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "perl ${DIR}/subscript/compInsDel.pl ${OUTPUTPATH}/tmp/temp.tumor.ins ${OUTPUTPATH}/tmp/temp.normal.ins ${OUTPUTPATH}/tmp/temp.tumor.depth ${OUTPUTPATH}/tmp/temp.normal.depth ${MIN_TUMOR_DEPTH} ${MIN_NORMAL_DEPTH} ${MIN_TUMOR_VARIANT_READ} ${MIN_TUMOR_ALLELE_FREQ} ${MAX_NORMAL_ALLELE_FREQ} > ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.filt"
perl ${DIR}/subscript/compInsDel.pl ${OUTPUTPATH}/tmp/temp.tumor.ins ${OUTPUTPATH}/tmp/temp.normal.ins ${OUTPUTPATH}/tmp/temp.tumor.depth ${OUTPUTPATH}/tmp/temp.normal.depth ${MIN_TUMOR_DEPTH} ${MIN_NORMAL_DEPTH} ${MIN_TUMOR_VARIANT_READ} ${MIN_TUMOR_ALLELE_FREQ} ${MAX_NORMAL_ALLELE_FREQ} > ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.filt
check_error $?
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "perl ${DIR}/subscript/compInsDel.pl ${OUTPUTPATH}/tmp/temp.tumor.del ${OUTPUTPATH}/tmp/temp.normal.del ${OUTPUTPATH}/tmp/temp.tumor.depth ${OUTPUTPATH}/tmp/temp.normal.depth ${MIN_TUMOR_DEPTH} ${MIN_NORMAL_DEPTH} ${MIN_TUMOR_VARIANT_READ} ${MIN_TUMOR_ALLELE_FREQ} ${MAX_NORMAL_ALLELE_FREQ} > ${OUTPUTPATH}/tmp/temp.tumor_normal.del.filt"
perl ${DIR}/subscript/compInsDel.pl ${OUTPUTPATH}/tmp/temp.tumor.del ${OUTPUTPATH}/tmp/temp.normal.del ${OUTPUTPATH}/tmp/temp.tumor.depth ${OUTPUTPATH}/tmp/temp.normal.depth ${MIN_TUMOR_DEPTH} ${MIN_NORMAL_DEPTH} ${MIN_TUMOR_VARIANT_READ} ${MIN_TUMOR_ALLELE_FREQ} ${MAX_NORMAL_ALLELE_FREQ} > ${OUTPUTPATH}/tmp/temp.tumor_normal.del.filt
check_error $?
# add information of normal reference
##########
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "perl ${DIR}/subscript/getRefNor_base.pl ${OUTPUTPATH}/tmp/temp.tumor_normal.base.filt ${REFERENCELIST} ${TH_BASE_QUAL_REF} ${TH_MAPPING_QUAL_REF} ${OUTPUTPATH}/tmp ${PATH_TO_SAMTOOLS} > ${OUTPUTPATH}/tmp/temp.tumor_normal.base.filt.ref"
perl ${DIR}/subscript/getRefNor_base.pl ${OUTPUTPATH}/tmp/temp.tumor_normal.base.filt ${REFERENCELIST} ${TH_BASE_QUAL_REF} ${TH_MAPPING_QUAL_REF} ${OUTPUTPATH}/tmp ${PATH_TO_SAMTOOLS} > ${OUTPUTPATH}/tmp/temp.tumor_normal.base.filt.ref
check_error $?
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "perl ${DIR}/subscript/getRefNor_insdel.pl ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.filt ${REFERENCELIST} 1 ${TH_MAPPING_QUAL_REF} ${OUTPUTPATH}/tmp ${PATH_TO_SAMTOOLS} > ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.filt.ref"
perl ${DIR}/subscript/getRefNor_insdel.pl ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.filt ${REFERENCELIST} 1 ${TH_MAPPING_QUAL_REF} ${OUTPUTPATH}/tmp ${PATH_TO_SAMTOOLS} > ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.filt.ref
check_error $?
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "perl ${DIR}/subscript/getRefNor_insdel.pl ${OUTPUTPATH}/tmp/temp.tumor_normal.del.filt ${REFERENCELIST} 2 ${TH_MAPPING_QUAL_REF} ${OUTPUTPATH}/tmp ${PATH_TO_SAMTOOLS} > ${OUTPUTPATH}/tmp/temp.tumor_normal.del.filt.ref"
perl ${DIR}/subscript/getRefNor_insdel.pl ${OUTPUTPATH}/tmp/temp.tumor_normal.del.filt ${REFERENCELIST} 2 ${TH_MAPPING_QUAL_REF} ${OUTPUTPATH}/tmp ${PATH_TO_SAMTOOLS} > ${OUTPUTPATH}/tmp/temp.tumor_normal.del.filt.ref
check_error $?
# caluculate p-value for each candidate by the Beta-binominal sequencing error model
##########
echo "`date '+%Y-%m-%d %H:%M:%S'`"
if [ ! -s ${OUTPUTPATH}/tmp/temp.tumor_normal.base.filt.ref ]; then
echo "make empty file : ${OUTPUTPATH}/tmp/temp.tumor_normal.base.eb"
rm -f ${OUTPUTPATH}/tmp/temp.tumor_normal.base.eb
touch ${OUTPUTPATH}/tmp/temp.tumor_normal.base.eb
else
echo "${PATH_TO_R}/R --vanilla --slave --args ${OUTPUTPATH}/tmp/temp.tumor_normal.base.filt.ref ${OUTPUTPATH}/tmp/temp.tumor_normal.base.eb < ${DIR}/subscript/proc_EBcall.R"
${PATH_TO_R}/R --vanilla --slave --args ${OUTPUTPATH}/tmp/temp.tumor_normal.base.filt.ref ${OUTPUTPATH}/tmp/temp.tumor_normal.base.eb < ${DIR}/subscript/proc_EBcall.R
check_error $?
fi
echo "`date '+%Y-%m-%d %H:%M:%S'`"
if [ ! -s ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.filt.ref ]; then
echo "make empty file : ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.eb"
rm -f ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.eb
touch ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.eb
else
echo "${PATH_TO_R}/R --vanilla --slave --args ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.filt.ref ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.eb < ${DIR}/subscript/proc_EBcall.R"
${PATH_TO_R}/R --vanilla --slave --args ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.filt.ref ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.eb < ${DIR}/subscript/proc_EBcall.R
check_error $?
fi
echo "`date '+%Y-%m-%d %H:%M:%S'`"
if [ ! -s ${OUTPUTPATH}/tmp/temp.tumor_normal.del.filt.ref ]; then
echo "make empty file : ${OUTPUTPATH}/tmp/temp.tumor_normal.del.eb"
rm -f ${OUTPUTPATH}/tmp/temp.tumor_normal.del.eb
touch ${OUTPUTPATH}/tmp/temp.tumor_normal.del.eb
else
echo "${PATH_TO_R}/R --vanilla --slave --args ${OUTPUTPATH}/tmp/temp.tumor_normal.del.filt.ref ${OUTPUTPATH}/tmp/temp.tumor_normal.del.eb < ${DIR}/subscript/proc_EBcall.R"
${PATH_TO_R}/R --vanilla --slave --args ${OUTPUTPATH}/tmp/temp.tumor_normal.del.filt.ref ${OUTPUTPATH}/tmp/temp.tumor_normal.del.eb < ${DIR}/subscript/proc_EBcall.R
check_error $?
fi
# merge and convert the format of three variation files (mutation, insertion and deletion) for Annovar
##########
echo "`date '+%Y-%m-%d %H:%M:%S'`"
echo "perl ${DIR}/subscript/procForAnnovar.pl ${OUTPUTPATH}/tmp/temp.tumor_normal.base.eb ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.eb ${OUTPUTPATH}/tmp/temp.tumor_normal.del.eb > ${OUTPUTPATH}/output.txt"
perl ${DIR}/subscript/procForAnnovar.pl ${OUTPUTPATH}/tmp/temp.tumor_normal.base.eb ${OUTPUTPATH}/tmp/temp.tumor_normal.ins.eb ${OUTPUTPATH}/tmp/temp.tumor_normal.del.eb > ${OUTPUTPATH}/output.txt
check_error $?
echo "`date '+%Y-%m-%d %H:%M:%S'`"
: <<'#__COMMENT_OUT__'
#__COMMENT_OUT__