DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
active 2025-02-21 → 2026-08-06 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 532 days from 2025-02-21 to 2026-08-06. Pushes: 8 total, peak 3 in a day. Pull requests: 1 total, peak 1 in a day. Issues: 109 total, peak 7 in a day. Comments: 233 total, peak 6 in a day. Stars: 177 total, peak 3 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 |
|---|---|---|---|---|
| kishwarshafin | 76 | 7 | 0 | 51 |
| pichuan | 51 | 1 | 0 | 34 |
| akolesnikov | 14 | 0 | 0 | 10 |
| lucasbrambrink | 10 | 0 | 0 | 8 |
| mr-eyes | 9 | 0 | 0 | 7 |
| AndrewCarroll | 7 | 0 | 0 | 6 |
| gevro | 7 | 0 | 0 | 5 |
| mustafamax | 7 | 0 | 0 | 5 |
| danielecook | 7 | 0 | 0 | 7 |
| Overcraft90 | 7 | 0 | 0 | 4 |
| ellisjj | 6 | 0 | 0 | 5 |
| gianfilippo | 6 | 0 | 0 | 2 |
| awgymer | 6 | 0 | 0 | 5 |
| taejun12 | 5 | 0 | 0 | 1 |
| anastasiatete444-lgtm | 5 | 0 | 0 | 2 |
| ASLeonard | 5 | 0 | 0 | 4 |
| doron-st | 4 | 0 | 0 | 2 |
| veenarajaraman | 4 | 0 | 0 | 3 |
| jmsalcido | 3 | 0 | 0 | 2 |
| JinHelin404 | 3 | 0 | 0 | 1 |
Recent activity
Latest issues, pull requests and releases
- Issue comment#1087pichuan2026-06-28 03:18perf: use jemalloc for make_examples in the runtime image
- Issue comment#1085pichuan2026-06-24 04:28Apple Silicon native port (v2) — native arm64 DeepVariant/DeepTrio/DeepSomatic/pangenome
- Issue comment#1081Passion-Zoey2026-06-12 02:16DeepVariant on BGI / DNBSEQ PE150 data — model suitability and QC guidance
- Issue comment#1078awgymer2026-06-01 03:14call_variants_outputs did not pass sanity check
- Issue#1071pichuan2026-05-16 02:27singularity v.10 ValueError: NOT_FOUND: Failed to load FASTA file [] and/or index file [] Please double check these files exist and are of the correct format.
- Issue#1075CC-Juniper2026-05-10 19:57Pangenome Aware Deepvariant Job Dies during gbz loading
- Issue comment#1075CC-Juniper2026-05-10 19:57Pangenome Aware Deepvariant Job Dies during gbz loading
- Issue comment#1071katiecdillon2026-04-15 05:52singularity v.10 ValueError: NOT_FOUND: Failed to load FASTA file [] and/or index file [] Please double check these files exist and are of the correct format.
- Issue comment#1071pichuan2026-04-15 05:43singularity v.10 ValueError: NOT_FOUND: Failed to load FASTA file [] and/or index file [] Please double check these files exist and are of the correct format.
- Issue comment#1071pichuan2026-04-15 05:36singularity v.10 ValueError: NOT_FOUND: Failed to load FASTA file [] and/or index file [] Please double check these files exist and are of the correct format.
- Issue comment#1071katiecdillon2026-04-15 05:32singularity v.10 ValueError: NOT_FOUND: Failed to load FASTA file [] and/or index file [] Please double check these files exist and are of the correct format.
- Issue#1071katiecdillon2026-04-15 03:33singularity v.10 ValueError: NOT_FOUND: Failed to load FASTA file [] and/or index file [] Please double check these files exist and are of the correct format.
- Issue#1060kishwarshafin2026-04-07 16:38Segmentation fault in make_examples when running DeepVariant 1.10.0 with PacBio HiFi BAM
- Issue comment#1059kishwarshafin2026-04-05 16:22DeepVariant segmentation fault
- Issue comment#834antomicblitz2026-03-28 23:25run DeepVariant on ARM64
- Issue comment#834amiura12026-03-28 23:11run DeepVariant on ARM64
- Issue#1067milenovic2026-03-26 04:20run_deeptrio.py: help says --sample_name_child is optional, but is actually required
- Issue comment#1063pichuan2026-03-22 06:12run_deepvariant --model_type=MASSEQ does not accept --regions as a file path
- Issue comment#1060pichuan2026-03-18 02:59Segmentation fault in make_examples when running DeepVariant 1.10.0 with PacBio HiFi BAM
- Issue comment#1055kishwarshafin2026-03-16 23:28Obviously homozygous variants are called as a heterozygous variant（GT value error）
- Issue comment#1060pichuan2026-03-14 02:46Segmentation fault in make_examples when running DeepVariant 1.10.0 with PacBio HiFi BAM
- Issue#1060pichuan2026-03-14 02:29Segmentation fault in make_examples when running DeepVariant 1.10.0 with PacBio HiFi BAM
- Issue comment#1056hudja2026-03-12 11:46Is it possible to reuse examples.tfrecords?
- Issue comment#1057gevro2026-03-10 14:12Deeptrio Segmentation fault
- Issue comment#1057gevro2026-03-10 02:54Deeptrio Segmentation fault
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 177 stars here means stars gained during the window, not the repo's star count.