Trio whole exome service scripts and documentation

bcbio_gnomad_install.sh

submit_trio_wes_aspera_download.sh
submit_trio_wes_lftp_download.sh

trio_wes_prepare_bcbio_config_crf.sh
trio_wes_prepare_bcbio_config.sh
trio_whole_exome_create_parameter_files.pl

submit_trio_wes_bcbio.sh

trio_whole_exome_parse_peddy_ped_csv.pl

compare_indi_vars_by_version.py
convert_DEC_to_v10.py
decipher_NHS_WES_trio.sh
downstream_setup.sh
extract_BED_CCDS_DDG2P.py
extract_trio_FAM_PRO_ID.py
filter_LQ_GT.py
full_process_NHS_WES_trio.sh
gather_NHS_WES_aff_probands_results.sh
gather_NHS_WES_quad_results.sh
gather_NHS_WES_trio_results.sh
generate_coverage_result_file.py
generate_DEC_IGV.py
generate_G2P_out_VCF.py
NHS_WES_check_PED_aff_probands.py
NHS_WES_check_PED_quad.py
NHS_WES_extract_shared_vars.py
NHS_WES_extract_trio_FAM_PRO_ID.py
NHS_WES_filter_LQ_GT.py
NHS_WES_generate_aff_sib_ped.py
NHS_WES_generate_coverage_result_file.py
NHS_WES_generate_DEC_IGV_aff_probands.py
NHS_WES_generate_DEC_IGV.py
NHS_WES_generate_DEC_IGV.py.v1
NHS_WES_generate_DEC_IGV.py_wrong_gene_trans
NHS_WES_generate_DEC_IGV_sib_from_quad.py
NHS_WES_generate_DEC_IGV_trio_from_quad.py
NHS_WES_generate_trio_ped.py
NHS_WES_generate_trio_VCF.py
NHS_WES_trio_cram_setup.sh
NHS_WES_trio_delete_BAM.sh
NHS_WES_trio_setup.sh
old_downstream_setup.sh
old_submit_downstream.sh
old_submit_trio_wes_aspera_download.sh
processing_setup.sh
process_NHS_WES_aff_probands.sh
process_NHS_WES_quad_full.sh
process_NHS_WES_quad.sh
process_NHS_WES_trio_before_BAMOUT.sh
process_NHS_WES_trio.sh
run_processing.sh
submit_depth_of_coverage_MQ20_BQ20.sh
submit_downstream.sh
test_process_NHS_WES_trio.sh
test_run_processing.sh

submit_trio_wes_cram_compression.sh
submit_trio_wes_family_checksums.sh
submit_trio_wes_project_checksums.sh

trio_whole_exome_bcbio_template.yaml
trio_whole_exome_config.sh
vcf_config.json.backup