ctDNA mutation pipeline

My test ctDNA pipeline. Do not use at your production environment.

External Prerequisites

hg19

Name		Name	Last commit message	Last commit date
Latest commit History 5 Commits
LICENSE		LICENSE
README.md		README.md
filter_vcf.py		filter_vcf.py
mapped_stats4bedFile.py		mapped_stats4bedFile.py
parse_fastp_jsonOut.py		parse_fastp_jsonOut.py
run1_fastq_qc.sh		run1_fastq_qc.sh
run2_bwa-mem_PE.sh		run2_bwa-mem_PE.sh
run3_rmdup.sh		run3_rmdup.sh
run4_GATK_BQSR.sh		run4_GATK_BQSR.sh
run5_bamStats_old.sh		run5_bamStats_old.sh
run5_bam_stats.sh		run5_bam_stats.sh
run6_HaplotypeCaller_VQSR.sh		run6_HaplotypeCaller_VQSR.sh
run6_VariantFiltration.sh		run6_VariantFiltration.sh
run6_varscan2.sh		run6_varscan2.sh
run7_annovar.sh		run7_annovar.sh