Variant Calling and Postfiltering
Shell Perl Python R
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batch
remap
scripts
simulation
001_C_set_ref.sh
00_setup_project.sh
03_bam2fastq.sh
406_annotate2vcf.sh
407_vcf2ccf.sh
408_ccf2mysql.sh
50_cleanup.sh
61_annotator.sh
A01_quality_check_raw.sh
A02_search_ref.sh VarCap 3.0 Aug 30, 2016
A02_setup_reference.sh
A03_prinseq-lite.sh
A03_trimmomatic.sh
A_batch_setup.sh
B01_set_mapping_index.sh
B02_mapping_bwamem.sh
B03_mapping_bwamem.sh
B03_mapping_bwamem_SE.sh
C01_calling.sh
C01_calling_SE.sh
C01_calling_cortex.sh
D01_collect_raw_variant_files.sh
D02_filter_vcf.sh
D02_filter_vcf_galaxy.sh
D03_filter_tags.sh
D03_sum_vcf.sh
E01_annotate2vcf.sh
E02_vcf2ccf.sh
E03_ccf2mysql.sh
F01_backup_vcfs.sh
H01_generate_popmix.sh
README.md
README_CHANGES.txt
README_varcap_3.0.txt
ccf_id.txt
patch_process.sh
program.config
remove_bam_fq.sh
remove_caller.sh
remove_filter_caller.sh
variant.config

README.md