├── 1.QC.sh ├── 2.mapping.sh ├── 3.dedup.sh ├── 4.downsample.sh ├── 5.run_merge.sh ├── 6.index_bam.sh ├── 7.run_sompy.sh ├── GATK ├── 1.bqsr1.report.py ├── 2.bqsr.2.bqsr.py ├── 3.multiprocess_mutect2.py ├── BQSR1.sh ├── BQSR2.sh └── mutect2.sh ├── README.md ├── Strelka ├── 1.batch_manta.py ├── 2.batch_streka_somatic.py ├── README.md ├── Strelka.germline ├── Strelka.sh ├── getmanta.sh ├── getpy.sh └── manta.sh ├── batch_extract.py ├── ex_region.sort.bed.gz ├── multiprocess_index_bam.py └── multiprocess_merge.py /1.QC.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/1.QC.sh -------------------------------------------------------------------------------- /2.mapping.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/2.mapping.sh -------------------------------------------------------------------------------- /3.dedup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/3.dedup.sh -------------------------------------------------------------------------------- /4.downsample.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/4.downsample.sh -------------------------------------------------------------------------------- /5.run_merge.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/5.run_merge.sh -------------------------------------------------------------------------------- /6.index_bam.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/6.index_bam.sh -------------------------------------------------------------------------------- /7.run_sompy.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/7.run_sompy.sh -------------------------------------------------------------------------------- /GATK/1.bqsr1.report.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/GATK/1.bqsr1.report.py -------------------------------------------------------------------------------- /GATK/2.bqsr.2.bqsr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/GATK/2.bqsr.2.bqsr.py -------------------------------------------------------------------------------- /GATK/3.multiprocess_mutect2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/GATK/3.multiprocess_mutect2.py -------------------------------------------------------------------------------- /GATK/BQSR1.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/GATK/BQSR1.sh -------------------------------------------------------------------------------- /GATK/BQSR2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/GATK/BQSR2.sh -------------------------------------------------------------------------------- /GATK/mutect2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/GATK/mutect2.sh -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/README.md -------------------------------------------------------------------------------- /Strelka/1.batch_manta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/Strelka/1.batch_manta.py -------------------------------------------------------------------------------- /Strelka/2.batch_streka_somatic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/Strelka/2.batch_streka_somatic.py -------------------------------------------------------------------------------- /Strelka/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/Strelka/README.md -------------------------------------------------------------------------------- /Strelka/Strelka.germline: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Strelka/Strelka.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/Strelka/Strelka.sh -------------------------------------------------------------------------------- /Strelka/getmanta.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/Strelka/getmanta.sh -------------------------------------------------------------------------------- /Strelka/getpy.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/Strelka/getpy.sh -------------------------------------------------------------------------------- /Strelka/manta.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/Strelka/manta.sh -------------------------------------------------------------------------------- /batch_extract.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/batch_extract.py -------------------------------------------------------------------------------- /ex_region.sort.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/ex_region.sort.bed.gz -------------------------------------------------------------------------------- /multiprocess_index_bam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/multiprocess_index_bam.py -------------------------------------------------------------------------------- /multiprocess_merge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zic12345/SR2019/HEAD/multiprocess_merge.py --------------------------------------------------------------------------------