| 1234567891011121314151617181920212223242526272829303132333435363738 |
- #!/bin/sh
- #PBS -N concordance
- #PBS -j oe
- #PBS -l ncpus=12
- #PBS -l nodes=1
- #PBS -l mem=20G
- source /home/liuxiangqiong/miniconda3/bin/activate base
- target=/cgdata/liuxiangqiong/work62pancancer/Client/v0/script/refdata/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed
- ref=/cgdata/Database/GATK/b37/human_g1k_v37_decoy.fasta
- ###创建路径
- outputdir=${inputpath}/tempfile/pair_identify
- function run_mkcurrent_dir(){
- if [ ! -d "$outputdir" ]; then
- mkdir $outputdir
- fi
- }
- run_mkcurrent_dir;
- #获得tumor的target区域的pileup
- tumor_bam=${bam_dir}/${tumor}_clean.bam
- gatk Pileup \
- -R $ref \
- -L $target \
- -I $tumor_bam \
- -verbose \
- -O ${outputdir}/${tumor}.pileup
- #获得normal的target区域的pileup
- normal_bam=${bam_dir}/${normal}_clean.bam
- gatk Pileup \
- -R $ref \
- -L $target \
- -I $normal_bam \
- -verbose \
- -O ${outputdir}/${normal}.pileup
- ##一致性判断
- python3 /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/20220705/verify_concordance_v0.py -T ${outputdir}/${tumor}.pileup -N ${outputdir}/${normal}.pileup -H -O ${outputdir}/${sample}_concordance.txt
- #删除中间文件
- rm -rf ${outputdir}/${tumor}.pileup
- rm -rf ${outputdir}/${normal}.pileup
|
