{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":421876863,"defaultBranch":"main","name":"variant-analysis","ownerLogin":"allytrope","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2021-10-27T15:39:02.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/68163909?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1635349143.474019","currentOid":""},"activityList":{"items":[{"before":"ecbe3746e0a57014c6cfa372dac08b8bced7a351","after":"f6ef4b6e38a0c997f82e78bf2fba953466365bb6","ref":"refs/heads/main","pushedAt":"2024-05-10T20:31:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Update population.ipynb","shortMessageHtmlLink":"Update population.ipynb"}},{"before":"523b426f6571e510483fbe78c0043f0d89aaa4d4","after":"ecbe3746e0a57014c6cfa372dac08b8bced7a351","ref":"refs/heads/main","pushedAt":"2024-05-10T01:38:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Plot ROHs using scikit-allel","shortMessageHtmlLink":"Plot ROHs using scikit-allel"}},{"before":"45f54a50ae35e2959426129e9d396cb1a0b977cd","after":"523b426f6571e510483fbe78c0043f0d89aaa4d4","ref":"refs/heads/main","pushedAt":"2024-05-06T02:28:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Impove ROH plotting","shortMessageHtmlLink":"Impove ROH plotting"}},{"before":"7e5a788839d3588e5b3875a91c766264ff6669dc","after":"45f54a50ae35e2959426129e9d396cb1a0b977cd","ref":"refs/heads/main","pushedAt":"2024-05-04T17:40:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Change to bcftools for ROHs","shortMessageHtmlLink":"Change to bcftools for ROHs"}},{"before":"42e1f825aed8def2e373e069f73ea5f6e49fb8c9","after":"7e5a788839d3588e5b3875a91c766264ff6669dc","ref":"refs/heads/main","pushedAt":"2024-05-03T21:46:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Plot ROHs","shortMessageHtmlLink":"Plot ROHs"}},{"before":"b4eddc8d231d10eba14d680654834bba8945a8a9","after":"42e1f825aed8def2e373e069f73ea5f6e49fb8c9","ref":"refs/heads/main","pushedAt":"2024-05-02T20:08:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Create plots of population size and sequencing","shortMessageHtmlLink":"Create plots of population size and sequencing"}},{"before":"6c5a91071321250625785c1278c4002e6aab7675","after":"b4eddc8d231d10eba14d680654834bba8945a8a9","ref":"refs/heads/main","pushedAt":"2024-04-28T21:11:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Split out rules related to subsetting samples","shortMessageHtmlLink":"Split out rules related to subsetting samples"}},{"before":"a74bd7fb61b6c989dc29062eb9f0ccb1e2f8f512","after":"6c5a91071321250625785c1278c4002e6aab7675","ref":"refs/heads/main","pushedAt":"2024-04-15T19:51:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Plot population over time","shortMessageHtmlLink":"Plot population over time"}},{"before":"65ea715b137be97976ad5c064af6ca363ffd62f3","after":"a74bd7fb61b6c989dc29062eb9f0ccb1e2f8f512","ref":"refs/heads/main","pushedAt":"2024-04-08T16:59:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Better parallelize gVCFs, chromosome.list changes, other fixes\n\n- Simplify obtaining list of chromosomes\n- Move chromosomes.list and create on first run\n- Revert some uses of genocat that were not working\n- Fix read groups for alignment\n- gVCF creation is now split by chromosome","shortMessageHtmlLink":"Better parallelize gVCFs, chromosome.list changes, other fixes"}},{"before":"1c1897b6c22f3e7768b5296cc967f47f05e969f1","after":"65ea715b137be97976ad5c064af6ca363ffd62f3","ref":"refs/heads/main","pushedAt":"2024-03-19T02:43:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Split alignment rules into separate file","shortMessageHtmlLink":"Split alignment rules into separate file"}},{"before":"16d1f30c0bfbf5e1eff8eb56cc629ffacadd375d","after":"1c1897b6c22f3e7768b5296cc967f47f05e969f1","ref":"refs/heads/main","pushedAt":"2024-02-26T18:20:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Move filtering to config, fix BAM RG\n\n- Hard filtering is now read from config file\n- BAM RG field now pulls the sample name from the run name","shortMessageHtmlLink":"Move filtering to config, fix BAM RG"}},{"before":"6508c24dec8f8438d07f68111e46a94ccf225556","after":"16d1f30c0bfbf5e1eff8eb56cc629ffacadd375d","ref":"refs/heads/main","pushedAt":"2024-02-26T03:43:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Coverage rules and plots\n\n- Apply batch grouping to coverage rules\n- New rules determining exon coverage\n- Plot overall coverage across chromosomes\n- Plot exome coverage across batches","shortMessageHtmlLink":"Coverage rules and plots"}},{"before":"a76beb85f629d6687ae896fc37d07697b54e652f","after":"6508c24dec8f8438d07f68111e46a94ccf225556","ref":"refs/heads/main","pushedAt":"2024-02-23T18:14:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Modify structural_variants.smk\n\n- Split rules related to plotting alignments into own file\n- Using process substitution `<(...)` to stop writing merged BAMs to disk\n- SV calling consensus using SURVIVOR","shortMessageHtmlLink":"Modify structural_variants.smk"}},{"before":"f7d6c6564e1300fba3593873080d62128306d177","after":"a76beb85f629d6687ae896fc37d07697b54e652f","ref":"refs/heads/main","pushedAt":"2024-02-21T22:11:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Add --configfile option to README, rare variant tests","shortMessageHtmlLink":"Add --configfile option to README, rare variant tests"}},{"before":"e13a32c905fc365cd2675d409e0caf0aefc44f05","after":"f7d6c6564e1300fba3593873080d62128306d177","ref":"refs/heads/main","pushedAt":"2024-02-16T19:27:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Add config to command and script for summarizing samples","shortMessageHtmlLink":"Add config to command and script for summarizing samples"}},{"before":"fa0635009a3699d468b7e6cf270305ddd43aed65","after":"e13a32c905fc365cd2675d409e0caf0aefc44f05","ref":"refs/heads/main","pushedAt":"2024-02-09T18:02:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Introduce ability to take into account data from different batches\n\n- New config variable for determining whether runs from different batches should be treated as same sample\n- Add batch to results path for `alignments/` and `trimmed/`\n- Change `recalibrated/recal_tables/` to `recal_tables/`","shortMessageHtmlLink":"Introduce ability to take into account data from different batches"}},{"before":"b4eaf7ab92e047d4d3dfe1f093a16553e9fe073a","after":"fa0635009a3699d468b7e6cf270305ddd43aed65","ref":"refs/heads/main","pushedAt":"2024-01-30T20:26:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Use sample run instead of organism ID","shortMessageHtmlLink":"Use sample run instead of organism ID"}},{"before":"b638fd0031c2a913b6931aa539b8481950c0940a","after":"b4eaf7ab92e047d4d3dfe1f093a16553e9fe073a","ref":"refs/heads/main","pushedAt":"2023-12-20T19:51:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Improve SV processing and plot SVs","shortMessageHtmlLink":"Improve SV processing and plot SVs"}},{"before":"758932c4fb698207d56519d6f6dca7e34251b9e7","after":"b638fd0031c2a913b6931aa539b8481950c0940a","ref":"refs/heads/main","pushedAt":"2023-10-30T17:56:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Divergence and expected heterozygosity with plots","shortMessageHtmlLink":"Divergence and expected heterozygosity with plots"}},{"before":"31c0f4140f3e99fef4b6f5ac2e4809d4cc047e55","after":"758932c4fb698207d56519d6f6dca7e34251b9e7","ref":"refs/heads/main","pushedAt":"2023-09-12T21:33:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Calculate and graph Fst","shortMessageHtmlLink":"Calculate and graph Fst"}},{"before":"094fad840eb5d0d45e1528b26756699f68ba22ae","after":"31c0f4140f3e99fef4b6f5ac2e4809d4cc047e55","ref":"refs/heads/main","pushedAt":"2023-09-03T17:48:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Process WES and WGS separately during imputation","shortMessageHtmlLink":"Process WES and WGS separately during imputation"}},{"before":"d196bb4072e6f30d4cf8b55e091eb2162ce5e47b","after":"094fad840eb5d0d45e1528b26756699f68ba22ae","ref":"refs/heads/main","pushedAt":"2023-06-02T16:37:47.563Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Add admixture rules, mask discordant regions","shortMessageHtmlLink":"Add admixture rules, mask discordant regions"}},{"before":"ab42b5eb5421b94f37ddc3147d1d6b9f5f371eb9","after":"d196bb4072e6f30d4cf8b55e091eb2162ce5e47b","ref":"refs/heads/main","pushedAt":"2023-05-15T00:12:29.749Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Admixture plots","shortMessageHtmlLink":"Admixture plots"}},{"before":"48fa894024d8d8e3c99d946339b956fb4816b0a6","after":"ab42b5eb5421b94f37ddc3147d1d6b9f5f371eb9","ref":"refs/heads/main","pushedAt":"2023-03-11T04:25:16.519Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Plot heatmap for rate of inheritance of haplotypes","shortMessageHtmlLink":"Plot heatmap for rate of inheritance of haplotypes"}},{"before":"aacd710c89c3279dd575604689ace2f0ba46cc09","after":"48fa894024d8d8e3c99d946339b956fb4816b0a6","ref":"refs/heads/main","pushedAt":"2023-03-07T16:04:49.097Z","pushType":"push","commitsCount":1,"pusher":{"login":"allytrope","name":null,"path":"/allytrope","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/68163909?s=80&v=4"},"commit":{"message":"Add profile","shortMessageHtmlLink":"Add profile"}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"Y3Vyc29yOnYyOpK7MjAyNC0wNS0xMFQyMDozMTo0My4wMDAwMDBazwAAAARG6duB","startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wNS0xMFQyMDozMTo0My4wMDAwMDBazwAAAARG6duB","endCursor":"Y3Vyc29yOnYyOpK7MjAyMy0wMy0wN1QxNjowNDo0OS4wOTc4NjhazwAAAAL-V1Ab"}},"title":"Activity ยท allytrope/variant-analysis"}