steverozen/DBSverify
Analyze Next Generation Sequencing Data to Verify Somatic Double-BaseSubstituion (DBS) Calls

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Files in steverozen/DBSverify
Analyze Next Generation Sequencing Data to Verify Somatic Double-BaseSubstituion (DBS) Calls

.Rbuildignore
.gitignore
DBSverify.Rproj
DBSverify_0.10.pdf
DESCRIPTION
LICENSE.md
NAMESPACE
R/CategorizeReads.R R/CheckBAM.R R/CreateBAMSliceFileSamtools.R R/DBSConclusion.R R/DBS_conclusion_1_row.R R/GetAllBAMSlicesSamtools.R R/HMF_prep_1_BED_and_DBS_VCF.R R/HMF_prep_BEDs_and_DBS_VCFs.R R/IDVector.R R/PCAWG_fuse_sample_sheet_and_collab_manifest.R R/PCAWG_join_callers.R R/PCAWG_merge_DBS_calls_one_row.R R/PCAWG_merge_callers.R R/PCAWG_prep_BAM_list_and_BEDs.R R/PCAWG_prep_VCFs_and_BEDs_from_table.R R/PCAWG_prep_all_Collaboratory_VCFs_and_BEDs.R R/PCAWG_read_table_and_evaluate_DBS.R R/ReadDBSVCF.R R/ReadSamfile.R R/Read_DBS_VCF_and_BAMs_to_verify_DBSs.R R/Read_SBS_VCF_and_BAMs_to_verify_DBSs.R R/RegressSamDirectory.R R/Remove_non_canonical_chromosomes.R R/Slice2ReadSupport.R R/SumarizeReadSupportFromSlices.R R/TestBAMAndSamtools.R R/VCF_to_BED.R R/VerifyDBSVcf.R R/create_IGV_snapshot_script.R R/for_PCWAG_create_IGV_snapshots.R R/join_old_and_new.R R/prep_DBS_and_adjacent_SBS.R R/remove_named_column.R R/test_create_IGV_snapshot_script.R README.md
data-raw/DBSverify.overview.pptx
data-raw/notes_on_mergeBed
data-raw/old-code/CopyOfReadSamfile.R data-raw/old-code/CopyOfinvestigate.4.caller.dbs.R data-raw/old-code/CreateBAMSlice.R data-raw/old-code/GetReadSupport.R
data-raw/old-code/IGV_batch_snapshot.pl
data-raw/old-code/IGV_batch_snapshot_example_input_for_old_perl_version.txt
data-raw/old-code/MNVverify_MELA.R data-raw/old-code/MNVverify_MELA2.R data-raw/old-code/PCAWG_test_13446fc4-9fa6-4bb3-a00a-b9265b41eb1.R data-raw/old-code/PCAWG_test_cdeda-6dc1-4f17-b853-72a68e5aa7e1.R data-raw/old-code/ReadVCFAndBAMsAndProcess_old.R data-raw/old-code/SumarizeReadSupport.R data-raw/old-code/VerifyDBSVcf_old.R data-raw/old-code/investigate.4.caller.dbs.R data-raw/old-code/not.used.merge_DBS_calls_one_row.R data-raw/old-code/oldCreateBAMSliceFileSamtools.R data-raw/old-code/old_BAM.manifest.etc.R data-raw/old-code/old_DBSConclusion.R data-raw/old-code/old_DBS_conclusion_1_row.R data-raw/old-code/xx.GetPCAWGVAF.R data-raw/production_scripts/PCAWG_collab_set1_DBS_VCF_to_catalogs.R data-raw/production_scripts/PCAWG_collaboratory_set1_bis3.R data-raw/production_scripts/PCAWG_collaboratory_set2.R
data-raw/production_scripts/PCAWG_prep_DBS_VCF_and_BED_logs/out.qqq
data-raw/production_scripts/PCAWG_prep_DBS_VCF_and_BED_logs/out.xxx
data-raw/production_scripts/PCAWG_prep_DBS_VCF_and_BED_logs/out.yyy
data-raw/production_scripts/PCAWG_prep_DBS_VCF_and_BED_logs/out.zzz
data-raw/production_scripts/PCAWG_prep_all_Collaboratory_VCFs_and_BEDs_script.R data-raw/production_scripts/PCAWG_remove_rows_no_bed.R data-raw/production_scripts/check_num_bams_expected.R
data-raw/production_scripts/collab_score-client_bamSlice_v4.sh
data-raw/production_scripts/collaboratory_WGS_BAMS_repository_1623246282.tsv
data-raw/production_scripts/collaboratory_bams_2021_07_16.csv
data-raw/production_scripts/collaboratory_tables/collaboratory_bams_2021_07_13.csv
data-raw/production_scripts/collaboratory_tables/collaboratory_bams_2021_07_13_part2.csv
data-raw/production_scripts/collaboratory_tables/collaboratory_bams_2021_07_13_part3.csv
data-raw/production_scripts/collaboratory_tables/collaboratory_bams_2021_07_13_part4.csv
data-raw/production_scripts/collaboratory_tables/collaboratory_bams_full_2021_07_13.csv
data-raw/production_scripts/deal.with.normals.with.mutliple.tumors.R
data-raw/production_scripts/get.miniBAM.info.2021.08.03.csv
data-raw/production_scripts/multitumor.DBSverify.info.2021.08.03.csv
data-raw/production_scripts/notes-on-icgc.txt
data-raw/production_scripts/pcawg_sample_sheet.v1.4.2016-09-14.tsv
data-raw/production_scripts/sort_collaboratory_bam_slices.R data-raw/production_scripts/temporary_diff_evaled_vcfs.R data-raw/production_scripts/test_output/collab-set1-DBS.pdf
data-raw/short_collaboratory_bams.csv
inst/WORDLIST
man/CategorizeReads.Rd man/CreateBAMSliceFileSamtools.Rd man/DBSConclusion.Rd man/DBS_conclusion_1_row.Rd man/GetAllBAMSlicesSamtools.Rd man/PCAWG_prep_BAM_list_and_BEDs.Rd man/PCAWG_read_table_and_evaluate_DBS.Rd man/ReadSamfile.Rd man/Read_DBS_VCF_and_BAMs_to_verify_DBSs.Rd man/Read_SBS_VCF_and_BAMs_to_verify_DBSs.Rd man/RegressSAMDirectory.Rd man/Slice2ReadSupport.Rd man/VerifyDBSVcf.Rd tests/spelling.R tests/testthat.R
tests/testthat/input/1-116218637.vcf
tests/testthat/input/1-116218637.vcf_evaluated.vcf.regress
tests/testthat/input/1-30-DBS.vcf
tests/testthat/input/1-30-DBS.vcf_evaluated.vcf.regress
tests/testthat/input/1-30.vcf
tests/testthat/input/1-30.vcf_evaluated.vcf.regress
tests/testthat/input/1-74823446.vcf
tests/testthat/input/1-74823446.vcf.old
tests/testthat/input/1-74823446.vcf_evaluated.vcf.regress
tests/testthat/input/10-59377023.vcf
tests/testthat/input/10-59377023.vcf_evaluated.vcf.regress
tests/testthat/input/15-94501219.vcf
tests/testthat/input/15-94501219.vcf_evaluated.vcf.regress
tests/testthat/input/5-100759123.vcf
tests/testthat/input/5-100759123.vcf_evaluated.vcf.regress
tests/testthat/input/6-54496940.vcf
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tests/testthat/input/7-131714192.vcf
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tests/testthat/input/8-106268966.vcf
tests/testthat/input/8-106268966.vcf_evaluated.vcf.regress
tests/testthat/input/HepG2_AA1.vcf
tests/testthat/input/HepG2_AA1.vcf_evaluated.vcf.regress
tests/testthat/input/HepG2_AA1_DBS_evaluated.vcf
tests/testthat/input/HepG2_AA1_DBSlocs_Normal.bam
tests/testthat/input/HepG2_AA1_DBSlocs_Normal.bam.bai
tests/testthat/input/HepG2_AA1_DBSlocs_Tumor.bam
tests/testthat/input/HepG2_AA1_DBSlocs_Tumor.bam.bai
tests/testthat/input/bam_no_bai.bam
tests/testthat/input/long.test.N.slice.dir.regress/1-101371345.sam
tests/testthat/input/long.test.N.slice.dir.regress/1-110173437.sam
tests/testthat/input/long.test.N.slice.dir.regress/1-113307192.sam
tests/testthat/input/long.test.N.slice.dir.regress/1-114298882.sam
tests/testthat/input/long.test.N.slice.dir.regress/1-116218637.sam
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tests/testthat/input/long.test.N.slice.dir.regress/1-158549219.sam
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tests/testthat/input/long.test.N.slice.dir.regress/1-159978907.sam
tests/testthat/input/long.test.N.slice.dir.regress/1-165700378.sam
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tests/testthat/long.test.tmp.T.slice.dir/9-95653339.sam
tests/testthat/test_GetAllBAMSlicesSamtools.R tests/testthat/test_edge_cases.R tests/testthat/test_error_messages.R tests/testthat/test_long.R tests/testthat/test_saving_slices_from_GetAll....R tests/testthat/test_some_DBSconclusions.R tests/testthat/test_test_create_IGV_snapshot_script.R
steverozen/DBSverify documentation built on Dec. 23, 2021, 5:34 a.m.

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