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mutect2_template.sh
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mutect2_template.sh
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function parse_yaml {
local prefix=$2
local s='[[:space:]]*' w='[a-zA-Z0-9_]*' fs=$(echo @|tr @ '\034')
sed -ne "s|^\($s\):|\1|" \
-e "s|^\($s\)\($w\)$s:$s[\"']\(.*\)[\"']$s\$|\1$fs\2$fs\3|p" \
-e "s|^\($s\)\($w\)$s:$s\(.*\)$s\$|\1$fs\2$fs\3|p" $1 |
awk -F$fs '{
indent = length($1)/2;
vname[indent] = $2;
for (i in vname) {if (i > indent) {delete vname[i]}}
if (length($3) > 0) {
vn=""; for (i=0; i<indent; i++) {vn=(vn)(vname[i])("_")}
printf("%s%s%s=\"%s\"\n", "'$prefix'",vn, $2, $3);
}
}'
}
eval $(parse_yaml parameters.yaml)
printf "#Printing Mutect2 commands"
printf "\n"
printf "gatk Mutect2"
printf " --reference ${path_to_reference}" # what is this parameter
printf " --input ${working_directory}/${folder}/${output_bam_merged}.sorted.uniq.rg.bam" # what is this parameter
printf " --tumor-sample ${output_bam_merged}"
printf " --output ${working_directory}/${folder}/${output_bam_merged}_Mutect2.vcf"
printf " > ${working_directory}/${folder}/${output_bam_merged}.Mutect2.out 2>&1"
printf "\n"
printf "bcftools norm ${working_directory}/${folder}/${output_bam_merged}_Mutect2.vcf"
printf " --output ${working_directory}/${folder}/${output_bam_merged}_Mutect2_norm.vcf"
printf " --output-type v"
printf " -m \"-\""
printf "\n"
printf "rm ${working_directory}/${folder}/${output_bam_merged}_Mutect2.vcf"
printf "\n \n"