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Update DeepVariant and DeepTrio version to 1.8.0
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PiperOrigin-RevId: 698456404
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@kishwarshafin @copybara-github
kishwarshafin authored and copybara-github committed Nov 20, 2024
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2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -15,7 +15,7 @@ ARG FROM_IMAGE=ubuntu:22.04
# PYTHON_VERSION is also set in settings.sh.
ARG PYTHON_VERSION=3.10
ARG DV_GPU_BUILD=0
ARG VERSION=1.8.0-rc1
ARG VERSION=1.8.0
ARG TF_ENABLE_ONEDNN_OPTS=1

FROM continuumio/miniconda3 as conda_setup
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2 changes: 1 addition & 1 deletion Dockerfile.deepsomatic
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Expand Up @@ -15,7 +15,7 @@ ARG FROM_IMAGE=ubuntu:22.04
# PYTHON_VERSION is also set in settings.sh.
ARG PYTHON_VERSION=3.10
ARG DV_GPU_BUILD=0
ARG VERSION_DEEPSOMATIC=1.7.0
ARG VERSION_DEEPSOMATIC=1.8.0
ARG TF_ENABLE_ONEDNN_OPTS=1

FROM continuumio/miniconda3 as conda_setup
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2 changes: 1 addition & 1 deletion Dockerfile.deeptrio
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Expand Up @@ -15,7 +15,7 @@ ARG FROM_IMAGE=ubuntu:22.04
# PYTHON_VERSION is also set in settings.sh.
ARG PYTHON_VERSION=3.10
ARG DV_GPU_BUILD=0
ARG VERSION_DEEPTRIO=1.7.0
ARG VERSION_DEEPTRIO=1.8.0
ARG TF_ENABLE_ONEDNN_OPTS=1

FROM continuumio/miniconda3 as conda_setup
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32 changes: 19 additions & 13 deletions Dockerfile.pangenome_aware_deepvariant
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Expand Up @@ -15,7 +15,7 @@ ARG FROM_IMAGE=ubuntu:22.04
# PYTHON_VERSION is also set in settings.sh.
ARG PYTHON_VERSION=3.10
ARG DV_GPU_BUILD=0
ARG VERSION_DEEPVARIANT=1.7.0
ARG VERSION_DEEPVARIANT=1.8.0
ARG TF_ENABLE_ONEDNN_OPTS=1

FROM continuumio/miniconda3 AS conda_setup
Expand Down Expand Up @@ -116,18 +116,24 @@ RUN \
/opt/deepvariant/bin/load_gbz_into_shared_memory \
/opt/deepvariant/bin/run_pangenome_aware_deepvariant

# Copy models.
WORKDIR /opt/models/pangenome_aware_deepvariant/wgs
ADD https://storage.googleapis.com/brain-genomics/pichuan/share/deepvariant/models/PangenomeAwareDeepVariant/${VERSION_DEEPVARIANT}/wgs/weights-111-0.995872.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/brain-genomics/pichuan/share/deepvariant/models/PangenomeAwareDeepVariant/${VERSION_DEEPVARIANT}/wgs/weights-111-0.995872.ckpt.index .
ADD https://storage.googleapis.com/brain-genomics/pichuan/share/deepvariant/models/PangenomeAwareDeepVariant/${VERSION_DEEPVARIANT}/wgs/example_info.json .
RUN chmod -R +r /opt/models/pangenome_aware_deepvariant/wgs/*

WORKDIR /opt/models/pangenome_aware_deepvariant/wes
ADD https://storage.googleapis.com/brain-genomics/pichuan/share/deepvariant/models/PangenomeAwareDeepVariant/${VERSION_DEEPVARIANT}/wes/weights-31-0.987898.ckpt.data-00000-of-00001 .
ADD https://storage.googleapis.com/brain-genomics/pichuan/share/deepvariant/models/PangenomeAwareDeepVariant/${VERSION_DEEPVARIANT}/wes/weights-31-0.987898.ckpt.index .
ADD https://storage.googleapis.com/brain-genomics/pichuan/share/deepvariant/models/PangenomeAwareDeepVariant/${VERSION_DEEPVARIANT}/wes/example_info.json .
RUN chmod -R +r /opt/models/pangenome_aware_deepvariant/wes/*
# Copy models
WORKDIR opt/models/pangenome_aware_deepvariant/wgs
ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wgs.pagenome.savedmodel/fingerprint.pb .
ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wgs.pagenome.savedmodel/saved_model.pb .
ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wgs.pagenome.savedmodel/example_info.json .
WORKDIR opt/models/pangenome_aware_deepvariant/wgs/variables
ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wgs.pagenome.savedmodel/variables/variables.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wgs.pagenome.savedmodel/variables/variables.index .
RUN chmod -R +r opt/models/pangenome_aware_deepvariant/wgs/*

WORKDIR opt/models/pangenome_aware_deepvariant/wes
ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wes.pagenome.savedmodel/fingerprint.pb .
ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wes.pagenome.savedmodel/saved_model.pb .
ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wes.pagenome.savedmodel/example_info.json .
WORKDIR opt/models/pangenome_aware_deepvariant/wes/variables
ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wes.pagenome.savedmodel/variables/variables.data-00000-of-00001 .
ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wes.pagenome.savedmodel/variables/variables.index .
RUN chmod -R +r opt/models/pangenome_aware_deepvariant/wes/*

ENV PATH="${PATH}":/opt/conda/bin:/opt/conda/envs/bio/bin:/opt/deepvariant/bin/pangenome_aware_deepvariant:/opt/deepvariant/bin

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2 changes: 1 addition & 1 deletion deeptrio/testdata/HG002_ONT_deeptrio.denovo.examples.tfrecord.gz.example_info.json
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{"version": "1.7.0", "shape": [300, 199, 9], "channels": [1, 2, 3, 4, 5, 6, 7, 9, 10]}
{"version": "1.8.0", "shape": [300, 199, 9], "channels": [1, 2, 3, 4, 5, 6, 7, 9, 10]}
2 changes: 1 addition & 1 deletion deeptrio/testdata/HG002_ONT_deeptrio.examples.tfrecord.gz.example_info.json
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{"version": "1.7.0", "shape": [300, 199, 9], "channels": [1, 2, 3, 4, 5, 6, 7, 9, 10]}
{"version": "1.8.0", "shape": [300, 199, 9], "channels": [1, 2, 3, 4, 5, 6, 7, 9, 10]}
2 changes: 1 addition & 1 deletion deeptrio/testdata/alt_aligned_pileup.golden.training_examples.tfrecord.gz.example_info.json
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@@ -1 +1 @@
{"version": "1.7.0", "shape": [140, 199, 8], "channels": [1, 2, 3, 4, 5, 6, 9, 10]}
{"version": "1.8.0", "shape": [140, 199, 8], "channels": [1, 2, 3, 4, 5, 6, 9, 10]}
2 changes: 1 addition & 1 deletion deeptrio/testdata/customized_classes.golden.training_examples.tfrecord.gz.example_info.json
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@@ -1 +1 @@
{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deeptrio/testdata/golden.calling_examples.tfrecord.gz-00000-of-00003.example_info.json
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@@ -1 +1 @@
{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deeptrio/testdata/golden.calling_examples.tfrecord.gz-00001-of-00003.example_info.json
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@@ -1 +1 @@
{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deeptrio/testdata/golden.calling_examples.tfrecord.gz-00002-of-00003.example_info.json
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@@ -1 +1 @@
{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deeptrio/testdata/golden.calling_examples.tfrecord.gz.example_info.json
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{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deeptrio/testdata/golden.postprocess_gvcf_output.g.vcf
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Expand Up @@ -12,7 +12,7 @@
##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.7.0
##DeepVariant_version=1.8.0
##contig=<ID=20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT child
20 10000000 . T <*> 0 . END=10000011 GT:GQ:MIN_DP:PL 0/0:48:16:0,48,479
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2 changes: 1 addition & 1 deletion deeptrio/testdata/golden.postprocess_single_site_output.vcf
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Expand Up @@ -12,7 +12,7 @@
##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.7.0
##DeepVariant_version=1.8.0
##contig=<ID=20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT child
20 10000117 . C T 13.1 PASS . GT:GQ:DP:AD:VAF:PL 0/1:12:18:6,12:0.666667:12,0,20
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2 changes: 1 addition & 1 deletion deeptrio/testdata/golden.training_examples.tfrecord.gz-00000-of-00003.example_info.json
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{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deeptrio/testdata/golden.training_examples.tfrecord.gz-00001-of-00003.example_info.json
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{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deeptrio/testdata/golden.training_examples.tfrecord.gz-00002-of-00003.example_info.json
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{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deeptrio/testdata/golden.training_examples.tfrecord.gz.example_info.json
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{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deeptrio/testdata/golden.training_examples.vcf
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Expand Up @@ -12,7 +12,7 @@
##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.7.0
##DeepVariant_version=1.8.0
##contig=<ID=20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT child
20 10001019 . T G 0 . . GT:DP:AD:VAF 0/1:16:10,6:0.375
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2 changes: 1 addition & 1 deletion ...rio/testdata/golden.vcf_candidate_importer.calling_examples.tfrecord.gz.example_info.json
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{"version": "1.7.0", "shape": [140, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [140, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion ...io/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz.example_info.json
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{"version": "1.7.0", "shape": [140, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [140, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deepvariant/dv_vcf_constants.py
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Expand Up @@ -32,7 +32,7 @@
from third_party.nucleus.util import vcf_constants

# Current release version of DeepVariant.
DEEP_VARIANT_VERSION = '1.7.0'
DEEP_VARIANT_VERSION = '1.8.0'

# FILTER field IDs.
DEEP_VARIANT_PASS = 'PASS'
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2 changes: 1 addition & 1 deletion ...ariant/testdata/customized_classes.golden.training_examples.tfrecord.gz.example_info.json
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{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
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2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.allele_frequency_examples.tfrecord.gz.example_info.json
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{"version": "1.7.0", "shape": [100, 221, 8], "channels": [1, 2, 3, 4, 5, 6, 19, 8]}
{"version": "1.8.0", "shape": [100, 221, 8], "channels": [1, 2, 3, 4, 5, 6, 19, 8]}
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{"version": "1.7.0", "shape": [100, 221, 8], "channels": [1, 2, 3, 4, 5, 6, 9, 10]}
{"version": "1.8.0", "shape": [100, 221, 8], "channels": [1, 2, 3, 4, 5, 6, 9, 10]}
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{"version": "1.7.0", "shape": [300, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
{"version": "1.8.0", "shape": [300, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
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2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.calling_examples.tfrecord.gz-00000-of-00003.example_info.json
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{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
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2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.calling_examples.tfrecord.gz-00001-of-00003.example_info.json
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{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
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{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.calling_examples.tfrecord.gz.example_info.json
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{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
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2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.calling_examples.with_flags.tfrecord.gz.example_info.json
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{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.haploid_chr20.postprocess_gvcf_output.g.vcf
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##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.7.0
##DeepVariant_version=1.8.0
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 10000000 . T <*> 0 . END=10000116 GT:GQ:MIN_DP:PL 0/0:50:45:0,135,1349
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2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.haploid_chr20.postprocess_single_site_output.vcf
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##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.7.0
##DeepVariant_version=1.8.0
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 10000117 . C T 1.2 RefCall . GT:GQ:DP:AD:VAF:PL ./.:6:55:25,30:0.545455:0,97,5
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2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.pacbio_examples.tfrecord.gz.example_info.json
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{"version": "1.7.0", "shape": [100, 199, 9], "channels": [1, 2, 3, 4, 5, 6, 7, 9, 10]}
{"version": "1.8.0", "shape": [100, 199, 9], "channels": [1, 2, 3, 4, 5, 6, 7, 9, 10]}
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2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.postprocess_gvcf_output.g.vcf
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##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.7.0
##DeepVariant_version=1.8.0
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 10000000 . T <*> 0 . END=10000116 GT:GQ:MIN_DP:PL 0/0:50:45:0,135,1349
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2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.postprocess_gvcf_output.med_dp.g.vcf
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##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.7.0
##DeepVariant_version=1.8.0
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 10000000 . T <*> 0 . END=10000116 GT:GQ:MIN_DP:MED_DP:PL 0/0:50:45:58:0,135,1349
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##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.7.0
##DeepVariant_version=1.8.0
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 10000117 . C T 37.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:36:55:25,30:0.545455:37,0,42
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##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.7.0
##DeepVariant_version=1.8.0
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 10000117 . C T 37.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:36:55:25,30:0.545455:37,0,42
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{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 7]}
{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 7]}
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{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
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{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
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{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
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{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
17 changes: 9 additions & 8 deletions deepvariant/testdata/golden.training_examples.tfrecord.gz.run_info.pbtxt
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Expand Up @@ -3566,14 +3566,15 @@ labeling_metrics {
}
resource_metrics {
host_name: "host"
physical_core_count: 12
cpu_frequency_mhz: 4053.686458333332
total_memory_mb: 128668
wall_time_seconds: 1.2084436416625977
cpu_user_time_seconds: 9.866901
cpu_system_time_seconds: 6.787293
memory_peak_rss_mb: 684
write_bytes: 282624
physical_core_count: 32
cpu_frequency_mhz: 2449.9980000000014
total_memory_mb: 120736
wall_time_seconds: 1.1024963855743408
cpu_user_time_seconds: 9.656006
cpu_system_time_seconds: 6.691356
memory_peak_rss_mb: 553
read_bytes: 229376
write_bytes: 274432
}
stats {
num_examples: 49
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##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.7.0
##DeepVariant_version=1.8.0
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 10001019 . T G 0 . . GT:DP:AD:VAF 0/1:44:31,13:0.295455
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{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
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{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
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##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.7.0
##DeepVariant_version=1.8.0
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 59777010 . C CCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCA 0.5 NoCall . GT:GQ:DP:AD:VAF:PL ./.:0:0:0,0:0:0,0
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