These commits are when the Protocol Buffers files have changed: (only the last 100 relevant commits are shown)
| Commit: | 646b56b | |
|---|---|---|
| Author: | Genomics team in Google Health | |
| Committer: | Copybara-Service | |
Automated Code Change PiperOrigin-RevId: 863568074
The documentation is generated from this commit.
| Commit: | 5fa43db | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add flag to disable graph pruning. PiperOrigin-RevId: 859824534
| Commit: | 51bb84e | |
|---|---|---|
| Author: | shafin | |
| Committer: | Copybara-Service | |
Add low VAF filtering to make_examples_core. PiperOrigin-RevId: 847854660
| Commit: | 5128eba | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
See https://github.com/google/deepvariant/pull/1026 for the review from and discussion with @doron-st. This change adds three new channels to DeepVariant to improve variant calling by incorporating specialized quality scores for homopolymer-related errors. These channels were implemented by Ultima Genomics, and incorporated into DeepVariant codebase now. PiperOrigin-RevId: 831122436
| Commit: | 550286b | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Refine indel allele fraction thresholds in variant calling. PiperOrigin-RevId: 811466153
| Commit: | 78f601d | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add support for using rejected alleles in DeepVariant. PiperOrigin-RevId: 803616117
| Commit: | 45c3c79 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Reduce `min_indel_allele_fraction` for large indels in VSC. PiperOrigin-RevId: 803604749
| Commit: | dd64de0 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Uses haplotype information from normal to 'project' and set phase information in the tumor, rather than doing so independently. PiperOrigin-RevId: 801031036
| Commit: | 6809600 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Make `kMinAllelesToPhase` a flag. PiperOrigin-RevId: 799657655
| Commit: | e575f1d | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add a combined labeler that combines positional and haplotype labeling. PiperOrigin-RevId: 791301622
| Commit: | 79b508a | |
|---|---|---|
| Author: | unda | |
| Committer: | Copybara-Service | |
Add AlleleSampleProbability channel definition. PiperOrigin-RevId: 789158110
| Commit: | 19bbe75 | |
|---|---|---|
| Author: | Genomics team in Google Health | |
| Committer: | Copybara-Service | |
Automated Code Change PiperOrigin-RevId: 781846941
| Commit: | 51c6059 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Add a channel for marking supplementary reads. PiperOrigin-RevId: 781092103
| Commit: | 27444cc | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] Allows GQ tuning, an execution mode in which `DeepVariant` produces a VCF for all GQ thresholds provided by `--small_model_gq_values`. It does so by calling all examples using both the `small_model` and `deepvariant`, and then resolving the CVO pairs during `postprocess_variants`. This is a very efficient way of tuning GQ thresholds. PiperOrigin-RevId: 772581096
| Commit: | 9e04ba3 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add fuzzy read support channel. PiperOrigin-RevId: 770754599
| Commit: | 4a786d2 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Add an optional --sort_by_alt_allele_support flag which allows the pileup image to be sorted by allele. The use case we have in mind is DeepSomatic, but we might try it in other use cases later on. This change is no-op by default. I double check that the unit test will fail if I set to: options_.set_sort_by_alt_allele_support(false); PiperOrigin-RevId: 767221677
| Commit: | 7201570 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Update DeepVariant to output allele-specific methylated sites. PiperOrigin-RevId: 760892375
| Commit: | f66b4f1 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[DeepVariant] Allows sample-specific alt_aligned_pileup setting. PiperOrigin-RevId: 758987782
| Commit: | 1118bd0 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Use bytes to store base qualities. PiperOrigin-RevId: 756482416
| Commit: | 83dbacc | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add option to output phasing error stats. PiperOrigin-RevId: 755109060
| Commit: | d12acb4 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Add a `--max_read_length_to_realign` flag to allow us to specify that (which defaults to 500). Refactor the `realign_reads` function to make it easier to read, but the logic stays the same. PiperOrigin-RevId: 755091025
| Commit: | 6660212 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Add a flag for optional filtering logic in window_selector.cc. PiperOrigin-RevId: 750779335
| Commit: | 4304445 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Adds the ability to write byte fields with nucleus. PiperOrigin-RevId: 747068559
| Commit: | e4a6326 | |
|---|---|---|
| Author: | farica | |
| Committer: | Copybara-Service | |
[DeepVariant] Extend merging of methylated sites to alt alleles PiperOrigin-RevId: 746146814
| Commit: | 59bb474 | |
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| Author: | farica | |
| Committer: | Copybara-Service | |
Implement foundation for iterative methylation-aware-phasing PiperOrigin-RevId: 743320949
| Commit: | 167550d | |
|---|---|---|
| Author: | farica | |
| Committer: | Copybara-Service | |
Exclude methylated ref sites in X and Y chromosomes for methylation-aware phasing PiperOrigin-RevId: 739016355
| Commit: | d6da5ac | |
|---|---|---|
| Author: | Genomics team in Google Health | |
| Committer: | Copybara-Service | |
Implement methylation-aware phasing support PiperOrigin-RevId: 738436840
| Commit: | 36bce4d | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] Expands the SM code to handle multiple samples. - tracks the `sample_name` in the `DeepVariantCall.ReadSupport` proto. - updates the `small_model_makes_examples` to compute the `BaseFeatures` per sample - update training code/configs to set the above params. PiperOrigin-RevId: 736249896
| Commit: | ed53c6d | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add `--output_debug_info` to control if extra debug info should be output. By default, it's False, to reduce the amount of log info. PiperOrigin-RevId: 735921061
| Commit: | 534ed69 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add non-uniform downsampling flags for DeepSomatic. PiperOrigin-RevId: 734640273
| Commit: | 4a01e8e | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Change window_selector logic. PiperOrigin-RevId: 734309163
| Commit: | f605fa7 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Add 6mA channel. PiperOrigin-RevId: 734230252
| Commit: | 5bf1d7f | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] Refactors how small model is instantiated in `make_examples`. This ties the variant caller to the `sample_lib.Sample`, similar to how each sample has its own reader. - moves `trained_small_model_path` to `make_examples.py` for each binary (currently DV and Pangenome-DV). - this is a no-op: everything should continue working as before. PiperOrigin-RevId: 734127195
| Commit: | 8dfe4f8 | |
|---|---|---|
| Author: | Genomics team in Google Health | |
| Committer: | Copybara-Service | |
Add methylation information to CVO PiperOrigin-RevId: 730626158
| Commit: | 15cc49c | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] Accept multi-allelic candidates * adds 2 `BaseFeatures`: `alt_indices_depth` and `alt_indices_variant_allele_frequency` * adds 2 `VariantFeatures`: `is_multiallelic` and `is_multiple_alt_alleles` features * adds field `make_examples_alt_allele_indices` to `DeepVariantCall` (the candidate proto), which instructs make_examples_native to restrict examples to the alt_allele_indices combinations that the small model did not call confidently. PiperOrigin-RevId: 726626783
| Commit: | 4e3b586 | |
|---|---|---|
| Author: | Genomics team in Google Health | |
| Committer: | Copybara-Service | |
Add option to enable methylation calling in DeepVariant PiperOrigin-RevId: 726141448
| Commit: | f32b5ef | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Move base modification parsing to nucleus. PiperOrigin-RevId: 723315638
| Commit: | d8b4083 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Part (4) of complex variants implementation. PiperOrigin-RevId: 722839178
| Commit: | 2b807f3 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
All realigning all regions. PiperOrigin-RevId: 722786313
| Commit: | 45318e2 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Add a 5mC methylation channel to deepvariant. PiperOrigin-RevId: 713528298
| Commit: | 05f0933 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Addressing the issue raised in https://github.com/google/deepvariant/issues/811 This change ensures that PL value is calculated according to the ploidy in reference blocks of gVCF. PiperOrigin-RevId: 698266848
| Commit: | f36f747 | |
|---|---|---|
| Author: | mobinasri | |
| Committer: | Copybara-Service | |
Fixing the memory issue with GBZ reader PiperOrigin-RevId: 695498239
| Commit: | 61777eb | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add phasing info to candidate output. PiperOrigin-RevId: 683811208
| Commit: | 2b1c194 | |
|---|---|---|
| Author: | mobinasri | |
| Committer: | Copybara-Service | |
- Fixed slowness in parsing alignments from gbz. The path index is now created when the gbzReader is instantiated instead of creating an index for each query. - Instead of hard-coding context size to 1k it is now set based on the partition_size - Added a flag `--ref_chrom_prefix` for adding a prefix to the chromosome names extracted from gbz file. It is needed when we have a reference like /cns/oz-d/home/brain-genomics/pichuan/b199781544/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.hprc_july7.fna whose chromosomes have the prefix of "GRCh38." - Renamed `pangenome_ref_name` to `ref_name_pangenome` since all other pangenome-related flags have `_pangenome` as suffix. - Removed printing runtimes in the query function of gbzReader PiperOrigin-RevId: 681641986
| Commit: | ca88780 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add an option to skip normalization in make_examples. PiperOrigin-RevId: 681532370
| Commit: | a87fd7a | |
|---|---|---|
| Author: | mobinasri | |
| Committer: | Copybara-Service | |
Added a GBZ reader to Nucleus and integrated it natively into make_examples for DeepVariant. The GBZ reader can be used to extract reads from a GBZ file. It can be slow at the moment and further optimizations will follow. PiperOrigin-RevId: 678760711
| Commit: | bfc5437 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] - Adds haplotype information to small model if `phase_reads` is enabled. - Add strand information as two features. PiperOrigin-RevId: 677840848
| Commit: | b4e1ab6 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add a sample option to skip phasing for a sample. PiperOrigin-RevId: 674437025
| Commit: | cff0882 | |
|---|---|---|
| Author: | Genomics team in Google Health | |
| Committer: | Copybara-Service | |
Automated Code Change PiperOrigin-RevId: 673655198
| Commit: | 6b74831 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | kishwarshafin | |
[small model] Enable the small model to call INDELs PiperOrigin-RevId: 663489298
| Commit: | 87f57dd | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | kishwarshafin | |
[small model] Capture additional signals (mapq, baseq, and context VAF) PiperOrigin-RevId: 657733223
| Commit: | 04f922c | |
|---|---|---|
| Author: | juancmier | |
| Committer: | kishwarshafin | |
Add functionality to blank out channels for a given variant type. PiperOrigin-RevId: 655808421
| Commit: | d2a279b | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | kishwarshafin | |
[small model] Fixes memory leak during small model inference PiperOrigin-RevId: 653710878
| Commit: | 5b3f233 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] Enable the small model to call INDELs PiperOrigin-RevId: 663489298
| Commit: | 50f4830 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] Capture additional signals (mapq, baseq, and context VAF) PiperOrigin-RevId: 657733223
| Commit: | 0fe7253 | |
|---|---|---|
| Author: | juancmier | |
| Committer: | Copybara-Service | |
Add functionality to blank out channels for a given variant type. PiperOrigin-RevId: 655808421
| Commit: | 348e2ce | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] Fixes memory leak during small model inference PiperOrigin-RevId: 653710878
| Commit: | c6ec0c9 | |
|---|---|---|
| Author: | juancmier | |
| Committer: | pichuan | |
Add mean coverage estimation per sample. * Gets the total possible regions using `UNION(RefContigs, SampleContigs) - ExcludeContigs` * Uses sampling rate to get a subset of total possible regions consecutively in the middle of the possible regions. This has been tested empirically to be fast and accurate but is subject to change. * Use allele counter to process reads in each region. Allele counter already performs logic to account for cigar operations counts reads at specific positions. PiperOrigin-RevId: 645466191
| Commit: | be4cc46 | |
|---|---|---|
| Author: | juancmier | |
| Committer: | pichuan | |
This CL adds a new channel to DeepVariant that contains the average coverage of the reads aligned to any given position or base in the genome. PiperOrigin-RevId: 643492127
| Commit: | e08da3e | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | pichuan | |
Adds `--skip_pileup_image_generation` to `make_examples` that determines if pileup images are also generated when generating small model examples. PiperOrigin-RevId: 641053022
| Commit: | 0b8f6da | |
|---|---|---|
| Author: | pichuan | |
| Committer: | pichuan | |
Add optional flags: exclude_variants_vcf_filename and exclude_variants_af_threshold. PiperOrigin-RevId: 638788722
| Commit: | 5a36126 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | pichuan | |
Add flag for downsampling training classes. PiperOrigin-RevId: 640646334
| Commit: | 76f727c | |
|---|---|---|
| Author: | shafin | |
| Committer: | pichuan | |
Internal change PiperOrigin-RevId: 636994465
| Commit: | 64d3775 | |
|---|---|---|
| Author: | koles | |
| Committer: | pichuan | |
make_example flags to support fast pipeline. PiperOrigin-RevId: 634539441
| Commit: | 42ba475 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | pichuan | |
Integrates small model variant calling with make_examples_core PiperOrigin-RevId: 625487979
| Commit: | 130b6bc | |
|---|---|---|
| Author: | pichuan | |
| Committer: | pichuan | |
Use the channels_enum_to_blank sample option in pangenome-aware implementation. PiperOrigin-RevId: 625533161
| Commit: | b0a1752 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | pichuan | |
Adds small model example generation code. PiperOrigin-RevId: 621262627
| Commit: | e154980 | |
|---|---|---|
| Author: | gjorge | |
| Committer: | pichuan | |
Small documentation fixes. PiperOrigin-RevId: 618323356
| Commit: | b693bbf | |
|---|---|---|
| Author: | danielecook | |
| Committer: | pichuan | |
Update DeepSomatic options proto. PiperOrigin-RevId: 613625838
| Commit: | d437bc8 | |
|---|---|---|
| Author: | koles | |
| Committer: | pichuan | |
Add --trim_reads_for_pileup flag. PiperOrigin-RevId: 610442006
| Commit: | 09193d8 | |
|---|---|---|
| Author: | mobinasri | |
| Committer: | pichuan | |
Pangenome aware calling PiperOrigin-RevId: 612593727
| Commit: | 0eba6d0 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | pichuan | |
In call_variants, if --include_debug_info is true, we'll incorporate the functionality in `vis.curate_pileup` to add extra annotations to the images. PiperOrigin-RevId: 603201809
| Commit: | 3fc2539 | |
|---|---|---|
| Author: | msamman | |
| Committer: | pichuan | |
remove base channels from pileup_image_native.cc PiperOrigin-RevId: 603467957
| Commit: | 83b69fe | |
|---|---|---|
| Author: | juancmier | |
| Committer: | Copybara-Service | |
Add mean coverage estimation per sample. * Gets the total possible regions using `UNION(RefContigs, SampleContigs) - ExcludeContigs` * Uses sampling rate to get a subset of total possible regions consecutively in the middle of the possible regions. This has been tested empirically to be fast and accurate but is subject to change. * Use allele counter to process reads in each region. Allele counter already performs logic to account for cigar operations counts reads at specific positions. PiperOrigin-RevId: 645466191
| Commit: | 8a36d86 | |
|---|---|---|
| Author: | juancmier | |
| Committer: | Copybara-Service | |
This CL adds a new channel to DeepVariant that contains the average coverage of the reads aligned to any given position or base in the genome. PiperOrigin-RevId: 643492127
| Commit: | 68e429e | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
Adds `--skip_pileup_image_generation` to `make_examples` that determines if pileup images are also generated when generating small model examples. PiperOrigin-RevId: 641053022
| Commit: | 48e95c6 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Add flag for downsampling training classes. PiperOrigin-RevId: 640646334
| Commit: | d96c5a8 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Add optional flags: exclude_variants_vcf_filename and exclude_variants_af_threshold. PiperOrigin-RevId: 638788722
| Commit: | 2c68cfe | |
|---|---|---|
| Author: | shafin | |
| Committer: | Copybara-Service | |
Internal change PiperOrigin-RevId: 636994465
| Commit: | 40a8cba | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
make_example flags to support fast pipeline. PiperOrigin-RevId: 634539441
| Commit: | 87ad5fc | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Use the channels_enum_to_blank sample option in pangenome-aware implementation. PiperOrigin-RevId: 625533161
| Commit: | aacaec8 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
Integrates small model variant calling with make_examples_core PiperOrigin-RevId: 625487979
| Commit: | 6991c56 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
Adds small model example generation code. PiperOrigin-RevId: 621262627
| Commit: | f91cc35 | |
|---|---|---|
| Author: | gjorge | |
| Committer: | Copybara-Service | |
Small documentation fixes. PiperOrigin-RevId: 618323356
| Commit: | 03df409 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | kishwarshafin | |
Resolve a trivial conflict in deepvariant.proto
| Commit: | e56cfa2 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Update DeepSomatic options proto. PiperOrigin-RevId: 613625838
| Commit: | 7f0f6ff | |
|---|---|---|
| Author: | mobinasri | |
| Committer: | Copybara-Service | |
Pangenome aware calling PiperOrigin-RevId: 612593727
| Commit: | 7a9df63 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add --trim_reads_for_pileup flag. PiperOrigin-RevId: 610442006
| Commit: | d8611fd | |
|---|---|---|
| Author: | msamman | |
| Committer: | Copybara-Service | |
remove base channels from pileup_image_native.cc PiperOrigin-RevId: 603467957
| Commit: | cc11840 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
In call_variants, if --include_debug_info is true, we'll incorporate the functionality in `vis.curate_pileup` to add extra annotations to the images. PiperOrigin-RevId: 603201809
| Commit: | 1a97858 | |
|---|---|---|
| Author: | yuchenzz | |
| Committer: | Pi-Chuan Chang | |
Add a new field in DebugInfo, so we can later add activation layers outputs. PiperOrigin-RevId: 600887239
| Commit: | 0afce8c | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Pi-Chuan Chang | |
Optionally set `deterministic` for SerializedToString, which can help the testdata creation more deterministic. Add a flag to set this value, but default is False (no-op). PiperOrigin-RevId: 579340935
| Commit: | 8e0dc61 | |
|---|---|---|
| Author: | yuchenzz | |
| Committer: | Copybara-Service | |
Add a new field in DebugInfo, so we can later add activation layers outputs. PiperOrigin-RevId: 600887239
| Commit: | dbd39b5 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Optionally set `deterministic` for SerializedToString, which can help the testdata creation more deterministic. Add a flag to set this value, but default is False (no-op). PiperOrigin-RevId: 579340935
| Commit: | 28c2a0a | |
|---|---|---|
| Author: | akiraly | |
| Committer: | kishwarshafin | |
Add encoded_image in DebugInfo. PiperOrigin-RevId: 571982144
| Commit: | a25a3d1 | |
|---|---|---|
| Author: | akiraly | |
| Committer: | Copybara-Service | |
Add encoded_image in DebugInfo. PiperOrigin-RevId: 571982144
| Commit: | 493b9d5 | |
|---|---|---|
| Author: | shafin | |
| Committer: | Pi-Chuan Chang | |
Add `de_novo` label in deepvariant examples for training with `sample_weight`. PiperOrigin-RevId: 544565682
| Commit: | ae6b749 | |
|---|---|---|
| Author: | shafin | |
| Committer: | Copybara-Service | |
Add `de_novo` label in deepvariant examples for training with `sample_weight`. PiperOrigin-RevId: 544565682
| Commit: | 30cac7f | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Pi-Chuan Chang | |
Add a `--output_sitelist` flag to DeepVariant. PiperOrigin-RevId: 528879605
| Commit: | 2eff181 | |
|---|---|---|
| Author: | koles | |
| Committer: | Pi-Chuan Chang | |
Exclude non-DNA regions larger than 300,000 bases. PiperOrigin-RevId: 520783371