Files · fd4bc70ddef2d2fe12ee513baa832e81021bc8ca · igmmbioinformatics / trio-whole-exome

Project id then version and date for config generation logs, copy PED file...

not populated not populated authored 3 years ago

Project id then version and date for config generation logs, copy PED file rather than symbolic links

fd4bc70d

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fd4bc70d 3 years ago

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Name	Last commit	Last update
docs
.gitignore
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_family_id_to_santosh_ped.pl
add_plate_and_family_id_to_ped.pl
bcbio_gnomad_install.sh
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_DEC_IGV.py
generate_G2P_out_VCF.py
generate_coverage_result_file.py
old_downstream_setup.sh
old_submit_downstream.sh
old_submit_trio_wes_aspera_download.sh
prepare_bcbio_config.sh
prepare_bcbio_config_crf.sh
prepare_bcbio_config_old_edge.sh
prepare_bcbio_config_santosh.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
processing_setup.sh
run_processing.sh
submit_bcbio_trio_wes.sh
submit_depth_of_coverage_MQ20_BQ20.sh
submit_downstream.sh
submit_trio_wes_archive_project.sh
submit_trio_wes_aspera_download.sh
submit_trio_wes_checksums.sh
submit_trio_wes_cram_compression.sh
submit_trio_wes_lftp_download.sh
submit_trio_wes_priority_and_qc_checksums.sh
test_process_NHS_WES_trio.sh
test_run_processing.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
trio_whole_exome_parse_peddy_ped_csv_no_batch.pl
vcf_config.json.backup

README.md