1234567891011121314151617181920212223242526272829303132333435363738394041424344454647484950515253545556575859606162636465666768697071727374757677787980818283848586878889 |
- #!/usr/bin/env bash
- ##Author: guochangquan
- ##Copyright 20210929
- ##company: NuProbe
- set -e
- function usage() {
- echo "Usage: $0 [ -s <sample> ] [ -i <fq_dir> ] [ -o <analysis_dir> ] [ -x <script_dir> ] [ -c <FeBY2_CNV_outdir> ]"
- echo "-s sample name"
- echo "-i input fastq dir"
- echo "-x script_dir"
- echo "-o analysis_dir"
- echo "-c FeBY2 CNV outdir"
- }
- if [ $# -eq 0 ]
- then
- usage
- exit
- fi
- feby2_script=$(cd "$(readlink -f "$0" | xargs dirname)"; pwd)
- while getopts ":s:c:x:o:i:h" opt; do
- case $opt in
- i)
- fq_dir=$OPTARG
- ;;
- o)
- out_dir=$OPTARG
- ;;
- s)
- sample=$OPTARG
- ;;
- c)
- cnv_dir=$OPTARG
- ;;
- x)
- feby2_script=$OPTARG
- ;;
- h)
- usage
- exit
- ;;
- \?)
- echo "Invalid option: -$OPTARG" > /dev/stderr
- usage
- exit
- ;;
- esac
- done
- echo "Input FASTQ dir:" $fq_dir
- echo "Output BAM dir:" $out_dir
- echo "Sample Name:" $sample
- echo "CNV Analysis dir:" $cnv_dir
- echo $feby2_script
- . $feby2_script/conf/feby2.cfg
- test -d $out_dir/${sample} || mkdir ${outdir}/${sample}
- cd $out_dir/${sample}
- ### FASTQ TRIM and Mapping
- sh $module/run_FQ2BAM_Speedseq.sh -s $sample -i $fq_dir -o $out_dir -x $feby2_script
- ### SNV/INDEL CAll and annotation
- sh $module/run_BAM2VCF_HC.sh -s $sample -o $out_dir -x $feby2_script
- ### QC
- sh $module/run_QC.sh -s $sample -o $out_dir -x $feby2_script
- ### yesuan
- sh $module/run_yesuan.sh -s $sample -o $out_dir -x $feby2_script
- ### prepare for CNV
- sh $module/run_CNV_prep.sh -s $sample -o $out_dir -x $feby2_script -c $cnv_dir
- ## for CNV
- cd $cnv_dir
- cp $feby2_script/dat/*.pcov $cnv_dir/
- cp $feby2_script/dat/ref.list $cnv_dir/
- perl $exe_dir/stats_chrs.pl FeBY2.chr.cov.xls && rm *.idxstats
- perl $exe_dir/com_cov_norm.pl FeBY2.exon.cov.xls
- ## CNV call
- sh $module/run_CNV_call.sh -s $sample -o $out_dir -x $feby2_script -c $cnv_dir
- ## Merge,Filter,Annotation,Plot
- sh $module/run_CNV_trim.sh -s $sample -o $out_dir -x $feby2_script -c $cnv_dir
|