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G2P.pm
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_DEC_IGV.py
NHS_WES_generate_DEC_IGV.py.v1
NHS_WES_generate_DEC_IGV.py_wrong_gene_trans
NHS_WES_generate_DEC_IGV_aff_probands.py
NHS_WES_generate_DEC_IGV_sib_from_quad.py
NHS_WES_generate_DEC_IGV_trio_from_quad.py
NHS_WES_generate_aff_sib_ped.py
NHS_WES_generate_coverage_result_file.py
NHS_WES_generate_trio_VCF.py
NHS_WES_generate_trio_ped.py
NHS_WES_trio_cram_setup.sh
NHS_WES_trio_delete_BAM.sh
NHS_WES_trio_setup.sh
README.md
add_plate_and_family_id_to_ped.pl
add_samples_from_previous_CRF_runs.sh
add_samples_from_previous_EdGe_runs.sh
bcbio_gnomad_install.sh
check_quad_PED.py
check_shared_PED.py
compare_indi_vars_by_version.py
convert_DEC_to_v10.py
decipher_NHS_WES_trio.sh
delete_BAM.sh
downstream_setup.sh
extract_BED_CCDS_DDG2P.py
extract_solo_FAM_PRO_ID.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
gather_quad_results.sh
gather_shared_results.sh
gather_solo_results.sh
gather_trio_results.sh
generate_DEC_IGV.py
generate_DEC_IGV_aff_sib_scripts_from_quad.py
generate_DEC_IGV_scripts.py
generate_DEC_IGV_shared_scripts.py
generate_DEC_IGV_solo_scripts.py
generate_DEC_IGV_trio_scripts_from_quad.py
generate_G2P_out_VCF.py
generate_aff_sib_PED_from_quad.py
generate_coverage_result_file.py
generate_trio_PED_from_quad.py
get_cov_output.py
old_downstream_setup.sh
old_submit_downstream.sh
old_submit_trio_wes_aspera_download.sh
process_NHS_WES_aff_probands.sh
process_NHS_WES_quad.sh
process_NHS_WES_quad_full.sh
process_NHS_WES_trio.sh
process_NHS_WES_trio_before_BAMOUT.sh
process_quad.sh
process_shared.sh
process_solo.sh
process_trio.sh
processing_setup.sh
run_processing.sh
submit_depth_of_coverage_MQ20_BQ20.sh
submit_downstream.sh
submit_trio_wes_aspera_download.sh
submit_trio_wes_bcbio.sh
submit_trio_wes_cram_compression.sh
submit_trio_wes_family_checksums.sh
submit_trio_wes_lftp_download.sh
submit_trio_wes_project_checksums.sh
submit_trio_wes_wget_download.sh
test_process_NHS_WES_trio.sh
test_run_processing.sh
trio_cram_setup.sh
trio_setup.sh
trio_wes_prepare_bcbio_config.sh
trio_wes_prepare_bcbio_config_crf.sh
trio_whole_exome_bcbio_template.yaml
trio_whole_exome_config.sh
trio_whole_exome_create_parameter_files.pl
trio_whole_exome_parse_peddy_ped_csv.pl
vcf_config.json.backup

Trio whole exome service scripts and documentation

Resources and set up

SOPs

Current script list by category

Resource generation & acquisition

bcbio_gnomad_install.sh

Sample acquisition

submit_trio_wes_aspera_download.sh
submit_trio_wes_lftp_download.sh

Alignment & variant calling

Preparation & config file generation

trio_wes_prepare_bcbio_config_crf.sh
trio_wes_prepare_bcbio_config.sh
trio_whole_exome_create_parameter_files.pl

Alignment & variant calling

submit_trio_wes_bcbio.sh

Quality control

trio_whole_exome_parse_peddy_ped_csv.pl

Prioritization

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

Archiving & cleanup

submit_trio_wes_cram_compression.sh
submit_trio_wes_family_checksums.sh
submit_trio_wes_project_checksums.sh

Configuration files

trio_whole_exome_bcbio_template.yaml
trio_whole_exome_config.sh
vcf_config.json.backup