1. deepSNV
  2. Graph
Graph of deepSNV
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • | *
  • | |\
  • | | *
  • * | |
  • | | *
  • * | |
  • * | |
  • * | |
  • |\ \ \
  • * | | |
  • | |_|/
  • |/| |
  • * | |
  • |\ \ \
  • | * | |
  • | * | |
  • | * | |
  • |/ / /
  • * | |
  • |\ \ \
  • | | * |
  • | | |/
  • | | *
  • | * |
  • | * |
  • |/ /
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • * |
  • * |
  • |\ \
  • | |/
  • |/|
  • | *
  • |/
  • | *
  • * |
  • |\ \
  • * | |
  • | * |
  • | |/
  • | *
  • |/
  • *
  • *
  • *
  • |\
  • | *
  • | *
  • | *
  • | *
  • | *
  • | *
  • |/
  • *
  • |\
  • * |
  • * |
  • |\ \
  • * | |
  • * | |
  • * | |
  • | * |
  • | * |
  • | | *
  • | | *
  • | | *
  • | | *
  • | | *
  • | |/
  • * |
  • * |
  • |\ \
  • | |/
  • |/|
  • | *
  • |/
  • *
  • *
  • *
  • *
  • |\
  • | *
  • * |
  • |\|
  • | *
  • | *
  • | |\
  • | * |
  • |/ /
  • | *
  • | |\
  • | |/
  • |/|
  • | | *
  • * | |
  • * | |
  • | |/
  • |/|
  • * |
  • | *
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • * |
  • |\ \
  • | | *
  • | * |
  • | | | *
  • | | |/
  • | |/|
  • | * |
  • | * |
  • | * |
  • * | |
  • * | |
  • * | |
  • | * |
  • | * |
  • | * |
  • | * |
  • 69c2512 (HEAD -> devel, origin/master, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 09:49:21 -0400;
  • 38615a9 (origin/RELEASE_3_18, RELEASE_3_18) bump x.y.z version to even y prior to creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 09:49:21 -0400;
  • b335f32 bump x.y.z version to odd y following creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 10:22:16 -0400;
  • 68b63ba (origin/RELEASE_3_17, RELEASE_3_17) bump x.y.z version to even y prior to creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 10:22:16 -0400;
  • 4241cbc bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:06:40 -0400;
  • a36f965 (origin/RELEASE_3_16, RELEASE_3_16) bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:06:40 -0400;
  • 712a30e Add NEWS entries and fix VariantAnnotation dependency version by John Marshall <John.W.Marshall@glasgow.ac.uk> 2022-05-31 22:07:28 +0100;
  • 9800af9 (origin/RELEASE_3_15, RELEASE_3_15) Merge recent bug fixes from the github/master branch by John Marshall <John.W.Marshall@glasgow.ac.uk> 2022-05-31 21:26:03 +0100;
  • 0baa80a Cherry-pick HTSlib 1.14 compatibility fix by John Marshall <John.W.Marshall@glasgow.ac.uk> 2022-05-31 17:15:19 +0100;
  • 3b904c4 Remove `FORMAT` from `#CHROM` line in template VCF files by John Marshall <John.W.Marshall@glasgow.ac.uk> 2022-05-31 17:15:19 +0100;
  • 818db37 Cherry-pick VariantAnnotation 1.42.1 compatibility fix by John Marshall <John.W.Marshall@glasgow.ac.uk> 2022-05-25 13:35:39 +0100;
  • 47d4f48 Add ##date DataFrame exactly as Rsamtools would produce it by John Marshall <John.W.Marshall@glasgow.ac.uk> 2022-05-25 13:35:39 +0100;
  • 3174fef Added John Marshall as contributor by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2022-05-18 13:06:37 +0200;
  • ced1a37 Merged with Bioconductor upstream by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2022-05-18 11:26:29 +0200;
  • 727182d Bump version after merge by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2022-05-18 11:24:07 +0200;
  • 4fd5b51 Merge pull request <a href="#16">#16</a> from jmarshall/no-NM-tag by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2022-05-17 09:18:31 +0200;
  • e8bc72d Filter by NM only on reads that do have an NM tag by John Marshall <John.W.Marshall@glasgow.ac.uk> 2022-05-16 14:52:28 +0100;
  • 1ed5fc4 Use sam_itr_queryi() instead of formatting a region string by John Marshall <John.W.Marshall@glasgow.ac.uk> 2022-05-16 14:31:31 +0100;
  • bb57949 Improve suggested flag mask and other minor documentation fixes by John Marshall <John.W.Marshall@glasgow.ac.uk> 2022-05-16 13:37:26 +0100;
  • 466abd2 Merge pull request <a href="#15">#15</a> from jmarshall/date-header by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2022-05-10 08:36:42 +0200;
  • 03a567a bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:10:15 +0000;
  • 8da9cbc bump x.y.z version to even y prior to creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:10:15 +0000;
  • d37752e Consruct VCFHeader in its final form instead of adding fields later by John Marshall <John.W.Marshall@glasgow.ac.uk> 2022-04-25 15:30:26 +0100;
  • 583aa81 Use VCFHeader methods to add a `##date` header by John Marshall <John.W.Marshall@glasgow.ac.uk> 2022-04-22 16:25:40 +0100;
  • e79bce8 bump x.y.z version to odd y following creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 16:01:57 +0000;
  • 875148c (origin/RELEASE_3_14, RELEASE_3_14) bump x.y.z version to even y prior to creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 16:01:57 +0000;
  • 48ebc6f bump x.y.z version to odd y following creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 15:51:24 +0000;
  • c542997 (origin/RELEASE_3_13, RELEASE_3_13) bump x.y.z version to even y prior to creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 15:51:24 +0000;
  • 492d0e0 bump x.y.z version to odd y following creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 10:44:43 -0400;
  • 20969f8 (origin/RELEASE_3_12, RELEASE_3_12) bump x.y.z version to even y prior to creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 10:44:43 -0400;
  • d48e0bf Call Rscript instead of R in Makevars by Hervé Pagès <hpages@fredhutch.org> 2020-07-14 13:14:58 -0700;
  • 437c1aa Bumped version after merging pull request by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-06-15 17:08:31 +0100;
  • 7890e86 Merge pull request <a href="#11">#11</a> from jmarshall/no-copy by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-06-15 17:06:54 +0100;
  • 6362cda No need to copy nttable each time bam2R_pileup_function() is called by John Marshall <John.W.Marshall@glasgow.ac.uk> 2020-06-11 17:14:21 +0100;
  • 80be4e4 (origin/RELEASE_3_11, RELEASE_3_11) Fixed issue when NM tag is absent by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-05-15 16:41:35 +0100;
  • 39bcc5a Merge branch 'master' of git@git.bioconductor.org:packages/deepSNV.git by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-05-18 15:00:31 +0100;
  • bf8ed6c Fixed issue when NM tag is absent by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-05-15 16:41:35 +0100;
  • cc98ae1 bump x.y.z version to odd y following creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:28:29 +0000;
  • 39327a9 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:28:29 +0000;
  • 91bfb6d Bumped version after merging pull request by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-03-26 15:56:54 +0000;
  • b169bfc Exclude Dockerfile from build by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-03-26 15:54:44 +0000;
  • 8e6af5d Merge pull request <a href="#10">#10</a> from rulixxx/master by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-03-26 15:53:40 +0000;
  • ea3c325 Added check for MN tag by ra11 <ra11@sanger.ac.uk> 2020-03-26 13:36:38 +0000;
  • a4da625 added missing ubuntu user by ra11 <ra11@sanger.ac.uk> 2020-03-25 20:48:15 +0000;
  • 8cbf78f updated help entry for bam2R by ra11 <ra11@sanger.ac.uk> 2020-03-25 18:47:30 +0000;
  • 4b1b8b5 added ubuntu user as default user for container by ra11 <ra11@sanger.ac.uk> 2020-03-25 17:08:16 +0000;
  • 5fe5516 Added mismatch filter in bam2R by ra11 <ra11@sanger.ac.uk> 2020-03-25 14:15:30 +0000;
  • 4ec12b1 Added a working Dockerfile by ra11 <ra11@sanger.ac.uk> 2020-03-24 19:57:01 +0000;
  • bd098c7 Merge remote-tracking branch 'git.bioconductor.org/master' by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-01-21 18:30:36 +0000;
  • c6b2711 Bumped to 1.33.2 by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-01-21 17:17:59 +0000;
  • f1170ec Merge pull request <a href="#9">#9</a> from drjsanger/feature/filter_bad_pairs by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-01-21 15:17:18 +0000;
  • 10c5f47 SystemRequirements: GNU make by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-01-21 14:42:24 +0000;
  • a118306 Added Makevars by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-01-21 14:02:29 +0000;
  • bb0625f Fixed build configuration for latest R/BioC by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2020-01-21 13:30:19 +0000;
  • 89e4282 Add keepflag parameter to bam2R function. Allows positive filtering of sam flags. Mask remains for exclusion filtering. by David Jones <drj@sanger.ac.uk> 2020-01-14 16:03:59 +0000;
  • d165df0 Add keepflag parameter to bam2R function. Allows positive filtering of sam flags. Mask remains for exclusion filtering. by David Jones <drj@sanger.ac.uk> 2020-01-14 15:28:17 +0000;
  • 97b4827 bump x.y.z version to odd y after creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:36:05 -0400;
  • 342a37e (origin/RELEASE_3_10, RELEASE_3_10) bump x.y.z version to even y prior to creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:08:27 -0400;
  • abfd64d Adjust Makevars.in and Makevars.win to work with latest Rhtslib by Hervé Pagès <hpages@fredhutch.org> 2019-10-12 13:04:32 -0700;
  • 378cf61 bump x.y.z versions to odd y after creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 12:11:10 -0400;
  • f598bac (origin/RELEASE_3_9, RELEASE_3_9) bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 11:53:34 -0400;
  • b6df9b1 Bumped version following merge by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2019-04-26 14:06:16 +0100;
  • 920c8b7 Merge pull request <a href="#8">#8</a> from drjsanger/feature/hts_lib_error by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2019-04-26 13:16:38 +0100;
  • 48f65de Add error checking to result of sam_itr_next by David Jones <drj@sanger.ac.uk> 2019-04-15 13:32:38 +0100;
  • c24823b Added missing #CHROM to vcf files by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2019-03-14 16:36:53 +0000;
  • 9d38935 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:30 -0400;
  • 9b6d747 (origin/RELEASE_3_8, RELEASE_3_8) bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:41:48 -0400;
  • 1c1a896 Merge branch 'devel' by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2018-10-05 15:43:18 +0100;
  • 09e8f21 Compatibility with VariantAnnotation_1.27.6 by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2018-10-05 15:41:44 +0100;
  • 8584c2d Overlapping read support by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2018-06-05 18:00:35 +0100;
  • 837ec36 Clean up; bump version by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2018-06-05 15:40:36 +0100;
  • 3e7004b Merge pull request <a href="#7">#7</a> from drjsanger/feature/add_overlapping_read_support by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2018-06-05 15:23:34 +0100;
  • 2703f83 Updated travis by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2018-06-05 14:02:05 +0100;
  • 88ccb04 Merge branch 'devel' into feature/add_overlapping_read_support by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2018-06-05 11:59:03 +0100;
  • 2fa8daa (origin/RELEASE_3_7, RELEASE_3_7) Bump version to trigger propagation of new Mac binary by Hervé Pagès <hpages@fredhutch.org> 2018-05-31 16:59:30 -0700;
  • 6504036 Path to htslib header files has changed in Rhtslib 1.13.1 by Hervé Pagès <hpages@fredhutch.org> 2018-05-22 19:01:38 -0700;
  • 8d654e2 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:41:38 -0400;
  • f16f0d3 bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:35:23 -0400;
  • d45c86a Added khash. Uses hash to store readname and base called on a per position basis. Where a read is encountered twice (overlapping read pairs) and the base is the same, the second is not added to the count. However if the base calls differ then a +1 is added for each different base call in this pair by drjsanger <drj@sanger.ac.uk> 2018-02-23 11:33:36 +0000;
  • da40fb8 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:52:13 -0400;
  • cfa5955 (origin/RELEASE_3_6, RELEASE_3_6) bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:39:38 -0400;
  • e5d4f00 Updated travis by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2017-10-17 16:44:29 +0100;
  • 0e44949 Decommissioned old devel branch by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2017-10-17 15:54:48 +0100;
  • 2399721 Roxygenised and checked in bioconductor/devel_base2:latest by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2017-10-17 14:54:10 +0100;
  • 4174870 Bumped version and updated travis by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2017-10-17 13:53:25 +0100;
  • 4fc0e88 Fix segfault on bioconductor Mac build by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2017-10-17 13:34:41 +0100;
  • 4e550d7 Merged with upstream/master by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2017-10-17 10:55:57 +0100;
  • ab771b2 Added support for overlapping read pairs by drjsanger <drj@sanger.ac.uk> 2017-09-29 12:08:05 +0100;
  • 5f0c9d7 bump x.y.z versions to odd y after creation of 3_5 branch by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:50:57 +0000;
  • c7ce3a8 (origin/RELEASE_3_5, RELEASE_3_5) Creating branch for BioC 3.5 release by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:45:44 +0000;
  • abc1e6d bump x.y.z versions to even y prior to creation of 3_5 branch by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:25:24 +0000;
  • 3771feb Bugfix: Comparison of pointer and 0 by Moritz Gerstung <gemoritz@ethz.ch> 2017-04-24 13:53:20 +0000;
  • 239445c Bump version by Moritz Gerstung <gemoritz@ethz.ch> 2017-04-24 13:53:12 +0000;
  • 28712c4 Bugfix: Comparison of pointer and 0 by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2017-03-27 19:12:34 +0100;
  • bb96d9a Bump version by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2017-03-28 09:36:56 +0100;
  • b9cff54 depends: rmarkdown by Moritz Gerstung <moritz.gerstung@ebi.ac.uk> 2017-03-27 19:12:34 +0100;
  • 0ea1084 Included new github site by Moritz Gerstung <gemoritz@ethz.ch> 2017-03-27 16:51:27 +0000;
  • 9b13a35 Bumped version and travis by Moritz Gerstung <gemoritz@ethz.ch> 2017-03-27 16:51:20 +0000;
  • 8b74e85 Updated URL by Moritz Gerstung <gemoritz@ethz.ch> 2017-03-27 16:51:12 +0000;
  • 4a9ac60 addition additional mapping quality filter by Moritz Gerstung <gemoritz@ethz.ch> 2017-03-27 16:51:04 +0000;