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doc
doc
 
 
etc
etc
 
 
.gitignore
.gitignore
 
 
Makefile
Makefile
 
 
README.md
README.md
 
 
SelfRelDepth.r
SelfRelDepth.r
 
 
SelfRelDepth.sh
SelfRelDepth.sh
 
 
SelfRelDepthtoHTML.py
SelfRelDepthtoHTML.py
 
 
_run_gbs_qc
_run_gbs_qc
 
 
addRun.sh
addRun.sh
 
 
add_sample_sheet_header.py
add_sample_sheet_header.py
 
 
ag_gbs_qc_prism.mk
ag_gbs_qc_prism.mk
 
 
ag_gbs_qc_prism.sh
ag_gbs_qc_prism.sh
 
 
annotateSelfRelDepth.py
annotateSelfRelDepth.py
 
 
annotate_sample_lowdepth.sh
annotate_sample_lowdepth.sh
 
 
autostart_gbs_qc
autostart_gbs_qc
 
 
barcode_yields_plots.r
barcode_yields_plots.r
 
 
batch_re_kgd.sh
batch_re_kgd.sh
 
 
check_demultiplex.py
check_demultiplex.py
 
 
collate_barcode_yields.py
collate_barcode_yields.py
 
 
collate_tags_reads.py
collate_tags_reads.py
 
 
count_tags.py
count_tags.py
 
 
debug_barcodes.sh
debug_barcodes.sh
 
 
deleteKeyfile.psql
deleteKeyfile.psql
 
 
delete_run_yields.psql
delete_run_yields.psql
 
 
demultiplex_example_1.sh
demultiplex_example_1.sh
 
 
demultiplex_example_2.sh
demultiplex_example_2.sh
 
 
demultiplex_prism.mk
demultiplex_prism.mk
 
 
demultiplex_prism.sh
demultiplex_prism.sh
 
 
dump_gbs_tables.psql
dump_gbs_tables.psql
 
 
fill_in_ref_indexes.psql
fill_in_ref_indexes.psql
 
 
fill_in_taxid.psql
fill_in_taxid.psql
 
 
genotype_prism.mk
genotype_prism.mk
 
 
genotype_prism.sh
genotype_prism.sh
 
 
get_cohort_count.psql
get_cohort_count.psql
 
 
get_cohort_count_from_database.sh
get_cohort_count_from_database.sh
 
 
get_cohort_from_database.sh
get_cohort_from_database.sh
 
 
get_dedupe_log.py
get_dedupe_log.py
 
 
get_flowcell_cohorts.psql
get_flowcell_cohorts.psql
 
 
get_historical_beta_plus.sh
get_historical_beta_plus.sh
 
 
get_kgd_version.sh
get_kgd_version.sh
 
 
get_reads_tags_per_sample.py
get_reads_tags_per_sample.py
 
 
get_run_samples.psql
get_run_samples.psql
 
 
get_snp_yield.py
get_snp_yield.py
 
 
get_snp_yield.sh
get_snp_yield.sh
 
 
import_hiseq_reads_tags_cv.psql
import_hiseq_reads_tags_cv.psql
 
 
import_hiseq_reads_tags_cv.sh
import_hiseq_reads_tags_cv.sh
 
 
import_kgd_stats.psql
import_kgd_stats.psql
 
 
import_kgd_stats.sh
import_kgd_stats.sh
 
 
is_keyfile_in_database.sh
is_keyfile_in_database.sh
 
 
is_run_in_database.sh
is_run_in_database.sh
 
 
keyfile_summary.psql
keyfile_summary.psql
 
 
listDBKeyfile.sh
listDBKeyfile.sh
 
 
list_keyfile.sh
list_keyfile.sh
 
 
list_keyfile_stub.py
list_keyfile_stub.py
 
 
make_clientcohort_pages.py
make_clientcohort_pages.py
 
 
make_cohort_pages.py
make_cohort_pages.py
 
 
merge_filtered_hapmap.py
merge_filtered_hapmap.py
 
 
nomerge_options_file.txt
nomerge_options_file.txt
 
 
patch_fastq.py
patch_fastq.py
 
 
ramify_tassel_keyfile.py
ramify_tassel_keyfile.py
 
 
reconcile_contaminants.py
reconcile_contaminants.py
 
 
replace_hiseq_samplesheet.c
replace_hiseq_samplesheet.c
 
 
reprocess_gbs_qc.sh
reprocess_gbs_qc.sh
 
 
rerun_legacy_library_example2.sh
rerun_legacy_library_example2.sh
 
 
run_GUSbase.R
run_GUSbase.R
 
 
run_gbs_qc
run_gbs_qc
 
 
run_gusbase.sh
run_gusbase.sh
 
 
run_kgd.R
run_kgd.R
 
 
run_kgd.sh
run_kgd.sh
 
 
sample_tags_sorted.sh
sample_tags_sorted.sh
 
 
sanitiseKeyFile.py
sanitiseKeyFile.py
 
 
sanitiseSampleSheet.py
sanitiseSampleSheet.py
 
 
schema.psql
schema.psql
 
 
setup_taxonomy.psql
setup_taxonomy.psql
 
 
snp_info_from_vcf.py
snp_info_from_vcf.py
 
 
summarise_read_and_tag_counts.py
summarise_read_and_tag_counts.py
 
 
tag_count_plots.r
tag_count_plots.r
 
 
updateFastQLocationInKeyFile.psql
updateFastQLocationInKeyFile.psql
 
 
update_hiseq_reads_tags_cv.psql
update_hiseq_reads_tags_cv.psql
 
 
update_kgd_stats.psql
update_kgd_stats.psql
 
 

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gbs_prism

gbs processing, q/c and visualisation

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refactored GBS processing

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