dnanexus-rnd / GLnexus

93%

master: 93%

LAST BUILD ON BRANCH v1.2.1

branch: v1.2.1

CHANGE BRANCH

x

Reset

• v1.2.1
• 1.1.12-1_add_max_allele_dv
• HEAD
• allow-N-ref
• bcf_bucket_cache
• bcf_bucket_cache_mt
• better-BCF-range-checks
• cli_command_iter_comp
• compare-2-impl-sampleset-range
• create_residuals_file
• delineation-unification-placeholders-v2
• enable_applet_residuals
• genomic_range_buckets
• gln-docker
• import_gvcf_thread_safety
• main
• master
• measure-loss
• measure-loss-debug
• measure_read_amp
• medium-tests
• mlin-AlleleDepthHelper-refactor
• mlin-BCFBucketCache
• mlin-BCFBucketCache-polishing
• mlin-BCFData-optimize-discover-alleles
• mlin-BCFKeyValueData-duplicate-danglers
• mlin-KeyValue-Iterator
• mlin-KeyValue-iterator-nocopy
• mlin-RocksKeyValue-prefix
• mlin-allele-info
• mlin-allele-target-range
• mlin-allele-unifier-v1
• mlin-backout-cache
• mlin-bcfreader-refactor
• mlin-bulk-insert-buffer
• mlin-call-two-overlapping-variants
• mlin-capnp-sites
• mlin-capnproto-0.7.0
• mlin-censor-nocall-format-fields
• mlin-config-yml
• mlin-deepvariant
• mlin-deepvariant-20181109
• mlin-depr-capnp
• mlin-detect-misaligned-indels
• mlin-disable-PL-validation
• mlin-discover-soft-copy-number
• mlin-discovered-alleles-yaml
• mlin-discovery-bias00
• mlin-discovery-unification-quality
• mlin-docker-pr-build
• mlin-dv-noncalled
• mlin-dv-partial-data
• mlin-dv-pl
• mlin-etl-folders
• mlin-fine-grain-RNC
• mlin-fix-unification-model
• mlin-format-fields
• mlin-format-from-info
• mlin-genotype-revision
• mlin-genotype-revision-ARCHIVED
• mlin-genotype-revision-simplified
• mlin-genotyper-beta2
• mlin-genotyper-log-stalls
• mlin-genotyper-rnc
• mlin-gvcf-manifest
• mlin-gvcf-symbolic-assumption
• mlin-inconsistent-trim
• mlin-issue168
• mlin-jemalloc-tuning
• mlin-measure-loss
• mlin-mem-thread-budgets
• mlin-memoize-all-samples-sampleset
• mlin-metadata-cache
• mlin-milestone1-cli
• mlin-min-dp
• mlin-minAQ2
• mlin-multistage-dockerfile
• mlin-multithread-query-test
• mlin-multithread-scalability
• mlin-multithread-scalability2
• mlin-overlap-compactions-discovery
• mlin-placeholder-gvcf-genotyper
• mlin-pseudo-ref-records
• mlin-range-bcf-end
• mlin-readme
• mlin-reduce-residuals
• mlin-ref-PL
• mlin-refactor-datacache-again
• mlin-refactor-ingestion-exceptions
• mlin-relax-unifier
• mlin-remove-loss-tracking
• mlin-reorder-format
• mlin-residual-containing-range
• mlin-revise-allele-pruning
• mlin-revise-homalt
• mlin-revise11
• mlin-rocksdb-upgrade
• mlin-rockskeyvalue
• mlin-rockskeyvalue-config
• mlin-sample-count
• mlin-sampleset-consistency
• mlin-sampleset-range
• mlin-service-abort-operations
• mlin-shorten-keys
• mlin-simplify-range_of_bcf
• mlin-skip-index
• mlin-spdlog
• mlin-squeeze
• mlin-star-allele
• mlin-strelka2
• mlin-travis-docker
• mlin-travis-modernization
• mlin-travis-release
• mlin-travis-valgrind
• mlin-trim-uncalled-alleles
• mlin-tweak-build
• mlin-unification-alt-dna
• mlin-unification-tests-1109
• mlin-unified-site-yaml-parser
• mlin-unifier-allele-frequencies
• mlin-unifier-max-alleles
• mlin-unifier-memory-usage
• mlin-unifier-prefer-small-alleles
• mlin-universal-compaction
• mlin-unrepresentable-symbolic-allele
• mlin-update-getting-started
• mlin-update-spdlog
• mlin-upgrade-capnp
• mlin-variant-qual
• mlin-weCall-calibration
• mlin-wecall
• mlin-wip
• mlin-workaround-neg-PL
• mlin-xAtlas-calibration
• mlin-xAtlas-wip
• mlin-xatlas
• mlin-zstd
• mlin/GxS
• mlin/dv-prior-calibration
• mlin/ghci
• mlin/test-gvcf-norm
• mlin/top2-half-calls
• mlin20160319
• mlin_minGQ
• one_pass
• orodeh-long-confidence-intervals
• orodeh-profiling
• orodeh-vcf-shard-merge
• orodeh-vcf-shard-merge-bgzip
• orodeh-vcf-shard-merge-mt-bgzip
• orodeh_allele_discovery_in_first_phase
• orodeh_capnp
• orodeh_capnp_debug
• orodeh_capnp_debug_II
• orodeh_capnp_debug_III
• orodeh_cleanup_unify_and_discover
• orodeh_config_param_for_new_subcommands
• orodeh_config_yaml_serialization
• orodeh_discovered_alleles_parallel_load
• orodeh_dynamic_jemalloc
• orodeh_ensure_jemelloc
• orodeh_experiments
• orodeh_expose_bucket_size_arg
• orodeh_gvcf_ingest_validation
• orodeh_lambda_predicate_for_queries
• orodeh_malloc_perf
• orodeh_malloc_static
• orodeh_mt_bgzip
• orodeh_one_db_pass_genotyper
• orodeh_perf_lxc
• orodeh_profiling
• orodeh_report_bad_yaml_file
• orodeh_separate_discover_phase
• orodeh_simple_public_cli
• orodeh_stream_yaml
• orodeh_unify_sites_as_stage
• orodeh_vcf_compare
• orodeh_yaml_stream_unify_sites
• perf_32_cpu
• perf_prof_with_bcf_cache
• performance_profiling
• profiling_WIP
• revert-111-orodeh_capnp_debug_III
• revert-122-mlin-skip-index
• split_ch2
• split_chrom
• split_gvcf_into_chromosomes
• tedyun-fixaq2zero
• test_travis_release
• translate-genotype-REF-check
• travis-master-pr-builds
• ubcf
• ubcf_cleanup
• unify_alleles_on_vector_inputs
• update_bgzip
• v0.1.0
• v0.2.0
• v0.3.0
• v0.3.1
• v0.3.2
• v0.3.3
• v0.5.0
• v0.5.x
• v0.6.1
• v1.0.0
• v1.0.1
• v1.0.2
• v1.1.0
• v1.1.1
• v1.1.10
• v1.1.11
• v1.1.12
• v1.1.12-1
• v1.1.2
• v1.1.3
• v1.1.4
• v1.1.5
• v1.1.6
• v1.1.7
• v1.1.8
• v1.1.9
• v1.1.x
• v1.2.0
• v1.2.0-pre.0
• v1.2.2
• v1.2.3
• v1.2.4
• v1.2.5
• v1.2.6
• v1.2.7
• vectorize_applet
• ymen-format-field-defaults
• ymen-format-field-ignore-ref
• ymen-format-fields
• ymen-format-fields-clear-on-rnc
• ymen-genotyper-v0.1
• ymen-genotyper-v1
• ymen-prep-for-genotype-v1
• ymen-trim-alts
• ymen-yaml-test-case
• ymen_genotyper_add_yml_tests
• zero_copy_bucket_scan

Build # 2081

Build Type

push

travis-ci

Committed by mlin

Commit Message

improve handling of DeepVariant non-called records

Compared to other callers, DeepVariant generates more non-called (./.) gVCF records to express uncertainty; including both reference bands and variant records. In 497277a5 we made sure to preserve the non-called status for reference bands, albeit in a heavy-handed way that censored all the QC fields (RNC=PartialData).

Here we introduce a new RNC InputNonCalled, used for both reference bands and variant records when applicable, which preserves the associated QC fields in the pVCF.

Run Details

4303 of 4607 relevant lines covered (93.4%)

947627.76 hits per line