consensus_indel.sh

#!/bin/bash
###
### generate consensus indel callset
###

function usage {
    >&2 echo "usage: $0 -b [/path/to/broad.indel.vcf.gz] -d [dkfz] -m [smufin] -s [sanger] -o [outfile: defaults to merged.vcf]"
    >&2 echo "       Generates consensus somatic indel VCFs for sample"
    >&2 echo "       Input VCFs must be bgzip-ed and tabix-ed."
    exit 1
}

readonly EXECUTABLE_PATH=${USE_EXECUTABLE_PATH:-"/usr/local/bin"}
readonly MODEL_PATH=${USE_MODEL_PATH:-"/usr/local/models"}
readonly TMPDIR=${USE_TMPDIR:-"/tmp"}

outfile=consensus.indel.vcf

while getopts "b:d:m:s:o:h" OPTION 
do
    case $OPTION in
        b) readonly broadfile="${OPTARG}"
            ;;
        d) readonly dkfzfile="${OPTARG}"
            ;;
        m) readonly smufinfile="${OPTARG}"
            ;;
        s) readonly sangerfile="${OPTARG}"
            ;;
        o) outfile="${OPTARG}"
            ;;
        h) usage
            ;;
    esac
done


##
## make sure required arguments are given
##
if [[ -z "$dkfzfile" ]] || [[ -z "$sangerfile" ]] 
then
    >&2 echo "required argument missing: need dkfz (-d) and sanger (-s) files"
    usage
fi

if [[ -z "${outfile}" ]]
then
    >&2 echo "Invalid empty output filename"
    usage
fi

if [[ ! -d "/dbs/annotation_databases" ]]
then
    >&2 echo "Missing directory containing needed annotations: /dbs/annotation_databases" 
    usage
fi

##
## make sure the files (look to be) bgzipped and have .tbi files
##
for file in "$smufinfile" "$broadfile" "$dkfzfile" "$sangerfile"
do
    if [[ ! -z "$file" ]] 
    then
        if [[ "$file" != *.gz ]] || [[ ! -f "${file}.tbi" ]]
        then
            >&2 echo "Input VCF files must be bgziped and tabixed."
            usage
        fi
    fi
done

##
## Merge indel calls
##
readonly MERGED="${TMPDIR}/merged.vaf.$$.indel.vcf"
readonly ANNOTATED="${TMPDIR}/annotated.indel.$$.vcf"
"${EXECUTABLE_PATH}"/merge-one-tumour-indel.sh \
    -b "${broadfile}" -d "${dkfzfile}" -m "${smufinfile}" -s "${sangerfile}" -o "$MERGED"

##
## Annotate with dbsnp, 1kgenomes, repeat_masker, and cosmic if provided
##

dbsnp_args=("${MERGED}.gz" "indel" "${ANNOTATED}")
"${EXECUTABLE_PATH}"/dbsnp_annotate_one.sh  "${dbsnp_args[@]}"

rm -f "${MERGED}"
rm -f "${MERGED}.gz"
rm -f "${MERGED}.gz.tbi"

##
## Filter with consensus model
##

if [[ -f $broadfile ]] && [[ -f $smufinfile ]]
then
    readonly MODELFILE="${MODEL_PATH}/stacked-logistic-all-four.RData"
elif [[ -f $broadfile ]] 
then
    readonly MODELFILE="${MODEL_PATH}/stacked-logistic-no-broad.RData"
else
    readonly MODELFILE="${MODEL_PATH}/stacked-logistic-no-smufin.RData"
fi

readonly INTERMEDIATE="${TMPDIR}/intermediate.indel.$$.vcf"
readonly MODEL_THRESHOLD=0.71
"${EXECUTABLE_PATH}"/apply_model.sh "${MODELFILE}" "${ANNOTATED}.gz" "${INTERMEDIATE}" "${outfile}" "$MODEL_THRESHOLD" 

 rm -f "${ANNOTATED}"*
 rm -f "${INTERMEDIATE}"*