Population-scale genotyping using pangenome graphs
active 2024-01-03 → 2025-12-31 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 729 days from 2024-01-03 to 2025-12-31. Pushes: 2 total, peak 1 in a day. Pull requests: 0 total, peak 0 in a day. Issues: 5 total, peak 1 in a day. Comments: 25 total, peak 3 in a day. Stars: 16 total, peak 2 in a day.
- Pushes
- Pull requests
- Issues
- Comments
- Stars
Stars, PRs, issues and forks are under-captured in the later part of this window. GH Archive progressively stopped capturing non-push events during 2026 — −95% or worse by the end of the window. Every series here except Pushes fades for that reason, so a decline above reflects the archive, not this repository. Pushes stay reliable throughout, so read them, and the contributor counts derived from them, as the real signal. Data health has the measurements.
Top contributors
Pushes, PRs, issues, reviews and comments — stars and forks excluded, so this is contribution rather than popularity
| Contributor | Contributions | Pushes | PRs | Comments |
|---|---|---|---|---|
| hannespetur | 8 | 2 | 0 | 6 |
| SunWinner01 | 3 | 0 | 0 | 3 |
| jjfarrell | 2 | 0 | 0 | 2 |
| likailong520 | 2 | 0 | 0 | 2 |
| tanger-code | 2 | 0 | 0 | 1 |
| Henry-Ding | 2 | 0 | 0 | 1 |
| Sreelekshmi-291 | 2 | 0 | 0 | 2 |
| weizhu365 | 2 | 0 | 0 | 2 |
| sroener | 1 | 0 | 0 | 1 |
| Lukecassar21 | 1 | 0 | 0 | 0 |
| nathanLauHKGI | 1 | 0 | 0 | 1 |
| kunmonster | 1 | 0 | 0 | 1 |
| realgoldace | 1 | 0 | 0 | 1 |
| zachary-foster | 1 | 0 | 0 | 0 |
| kuangzhuoran | 1 | 0 | 0 | 1 |
| dr-ashu-geno | 1 | 0 | 0 | 1 |
| JoannaTan | 1 | 0 | 0 | 0 |
Recent activity
Latest issues, pull requests and releases
- Issue comment#169kuangzhuoran2025-12-31 13:28When calling and genotyping SVs among very closely related populations, the false positive rate is very high.
- Issue comment#167hannespetur2025-09-26 15:36Negative count in genotype output of Graphtyper genotype_sv
- Issue comment#166jjfarrell2025-09-03 14:39Graphtyper vcf_merge failing with error code 139 for VCFs containing SVs
- Issue comment#166jjfarrell2025-08-31 21:22Graphtyper vcf_merge failing with error code 139 for VCFs containing SVs
- Issue comment#166sroener2025-08-21 12:24Graphtyper vcf_merge failing with error code 139 for VCFs containing SVs
- Issue comment#167hannespetur2025-08-19 15:28Negative count in genotype output of Graphtyper genotype_sv
- Issue comment#165realgoldace2025-08-04 03:15adding new samples to already generated vcf files of SNPs
- Issue comment#90Sreelekshmi-2912025-04-19 12:38Filtering graphtyper output results in losing 98% of SVs
- Issue comment#92weizhu3652025-01-10 01:54FILTER!=PASS but FT=PASS
- Issue comment#106weizhu3652025-01-09 00:18What does that mean？（FT=FAIL1/FAIL2/FAIL3！）
- Issue comment#146tanger-code2025-01-03 09:27In the genotype_sv result, the `REF` filed is N, and the `ALT` filed is not a sequence.
- Issue comment#144SunWinner012025-01-03 09:19REF in VCF file is N
- Issue comment#146SunWinner012025-01-03 09:13In the genotype_sv result, the `REF` filed is N, and the `ALT` filed is not a sequence.
- Issue comment#90likailong5202024-12-11 05:32Filtering graphtyper output results in losing 98% of SVs
- Issue comment#90likailong5202024-12-11 05:31Filtering graphtyper output results in losing 98% of SVs
- Issue comment#90kunmonster2024-11-21 00:50Filtering graphtyper output results in losing 98% of SVs
- Issue comment#157hannespetur2024-11-16 22:23question about “--sams=bam.list”
- Issue comment#157Henry-Ding2024-11-08 03:28question about “--sams=bam.list”
- Issue#157Henry-Ding2024-11-08 03:26question about “--sams=bam.list”
- Issue comment#90SunWinner012024-10-29 02:52Filtering graphtyper output results in losing 98% of SVs
- Issue comment#90dr-ashu-geno2024-10-29 02:44Filtering graphtyper output results in losing 98% of SVs
- Issue#156zachary-foster2024-10-17 00:03`graphtyper genotype` produces too many files for `graphtyper vcf_concatenate` to combine
- Issue comment#106Sreelekshmi-2912024-10-03 07:14What does that mean？（FT=FAIL1/FAIL2/FAIL3！）
- Issue comment#150nathanLauHKGI2024-05-27 01:06Created chopped CRAI
- Issue comment#149hannespetur2024-05-24 12:48( AC / NUM_MERGED_SVS ) < 25
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 16 stars here means stars gained during the window, not the repo's star count.