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DeepTrio whole genome sequencing case study

In this case study, we describe applying DeepTrio to a real WGS trio. Then we assess the quality of the DeepTrio variant calls with hap.py. In addition we evaluate a mendelian violation rate for a merged VCF.

To make it faster to run over this case study, we run only on chromosome 20.

Prepare environment

Tools

Docker will be used to run DeepTrio and hap.py,

Download Reference

We will be using GRCh38 for this case study.

mkdir -p reference

FTPDIR=ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids

curl ${FTPDIR}/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz | gunzip > reference/GRCh38_no_alt_analysis_set.fasta
curl ${FTPDIR}/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai > reference/GRCh38_no_alt_analysis_set.fasta.fai

Download Genome in a Bottle Benchmarks

We will benchmark our variant calls against v4.2 of the Genome in a Bottle small variant benchmarks for HG002, HG003, and HG004 trio.

mkdir -p benchmark

FTPDIR=ftp://ftp.ncbi.nlm.nih.gov//giab/ftp/data/AshkenazimTrio/analysis/NIST_v4.2_SmallVariantDraftBenchmark_07092020

curl ${FTPDIR}/HG002_GRCh38_1_22_v4.2_benchmark.bed > benchmark/HG002_GRCh38_1_22_v4.2_benchmark.bed
curl ${FTPDIR}/HG002_GRCh38_1_22_v4.2_benchmark.vcf.gz > benchmark/HG002_GRCh38_1_22_v4.2_benchmark.vcf.gz
curl ${FTPDIR}/HG002_GRCh38_1_22_v4.2_benchmark.vcf.gz.tbi > benchmark/HG002_GRCh38_1_22_v4.2_benchmark.vcf.gz.tbi

curl ${FTPDIR}/HG003_GRCh38_1_22_v4.2_benchmark.bed > benchmark/HG003_GRCh38_1_22_v4.2_benchmark.bed
curl ${FTPDIR}/HG003_GRCh38_1_22_v4.2_benchmark.vcf.gz > benchmark/HG003_GRCh38_1_22_v4.2_benchmark.vcf.gz
curl ${FTPDIR}/HG003_GRCh38_1_22_v4.2_benchmark.vcf.gz.tbi > benchmark/HG003_GRCh38_1_22_v4.2_benchmark.vcf.gz.tbi

curl ${FTPDIR}/HG004_GRCh38_1_22_v4.2_benchmark.bed > benchmark/HG004_GRCh38_1_22_v4.2_benchmark.bed
curl ${FTPDIR}/HG004_GRCh38_1_22_v4.2_benchmark.vcf.gz > benchmark/HG004_GRCh38_1_22_v4.2_benchmark.vcf.gz
curl ${FTPDIR}/HG004_GRCh38_1_22_v4.2_benchmark.vcf.gz.tbi > benchmark/HG004_GRCh38_1_22_v4.2_benchmark.vcf.gz.tbi

Download HG002, HG003, and HG004 BAM files

We'll use HG002, HG003, HG004 Illumina WGS reads publicly available from the PrecisionFDA Truth v2 Challenge.

mkdir -p input
HTTPDIR=https://storage.googleapis.com/deepvariant/case-study-testdata

curl ${HTTPDIR}/HG002.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam > input/HG002.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam
curl ${HTTPDIR}/HG002.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam.bai > input/HG002.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam.bai

curl ${HTTPDIR}/HG003.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam > input/HG003.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam
curl ${HTTPDIR}/HG003.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam.bai > input/HG003.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam.bai

curl ${HTTPDIR}/HG004.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam > input/HG004.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam
curl ${HTTPDIR}/HG004.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam.bai > input/HG004.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam.bai

Running DeepTrio with one command

DeepTrio pipeline consists of 4 steps: make_examples, call_variants, postprocess_variants and GLNexus merge. It is possible to run DeepTrio with one command using the run_deepvariant script. GLNexus is run as a separate command.

Running on a CPU-only machine

mkdir -p output
mkdir -p output/intermediate_results_dir

BIN_VERSION=1.0.1rc

time sudo docker run \
  -v "${PWD}/input":"/input"   \
  -v "${PWD}/output":"/output"  \
  -v "${PWD}/reference":"/reference" \
  gcr.io/deepvariant-docker/deeptrio:"${BIN_VERSION}" \
  /opt/deepvariant/bin/deeptrio/run_deeptrio \
  --model_type WGS \
  --ref /reference/GRCh38_no_alt_analysis_set.fasta \
  --reads_child /input/HG002.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam \
  --reads_parent1 /input/HG003.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam \
  --reads_parent2 /input/HG004.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam \
  --output_vcf_child /output/HG002.output.vcf.gz \
  --output_vcf_parent1 /output/HG003.output.vcf.gz \
  --output_vcf_parent2 /output/HG004.output.vcf.gz \
  --sample_name_child 'HG002' \
  --sample_name_parent1 'HG003' \
  --sample_name_parent2 'HG004' \
  --num_shards $(nproc)  \
  --regions chr20 \
  --intermediate_results_dir /output/intermediate_results_dir \
  --output_gvcf_child /output/HG002.g.vcf.gz \
  --output_gvcf_parent1 /output/HG003.g.vcf.gz \
  --output_gvcf_parent2 /output/HG004.g.vcf.gz

By specifying --model_type WGS, you'll be using a model that is best suited for Illumina Whole Genome Sequencing data.

--intermediate_results_dir flag is optional. By specifying it, the intermediate outputs of make_examples and call_variants stages can be found in the directory. After the command, you can find these files in the directory:

call_variants_output_child.tfrecord.gz
call_variants_output_parent1.tfrecord.gz
call_variants_output_parent2.tfrecord.gz

gvcf_child.tfrecord-?????-of-?????.gz
gvcf_parent1.tfrecord-?????-of-?????.gz
gvcf_parent2.tfrecord-?????-of-?????.gz

make_examples_child.tfrecord-?????-of-?????.gz
make_examples_parent1.tfrecord-?????-of-?????.gz
make_examples_parent2.tfrecord-?????-of-?????.gz

For running on GPU machines, or using Singularity instead of Docker, see Quick Start.

Merge VCFs using GLNexus

At this step we take all 3 VCFs generated in the previous step and merge them using GLNexus.

# BCFTools are required:
sudo apt-get -y install bcftools
sudo apt-get -y install tabix

sudo docker run \
  -v "${PWD}/output":"/output" \
  quay.io/mlin/glnexus:v1.2.7 \
  /usr/local/bin/glnexus_cli \
  --config DeepVariantWGS \
  /output/HG002.g.vcf.gz \
  /output/HG003.g.vcf.gz \
  /output/HG004.g.vcf.gz \
  | bcftools view - | bgzip -c > output/HG002_trio_merged.vcf.gz

After completion of GLNexus command we should have a new merged VCF file in the output directory.

HG002_trio_merged.vcf.gz

Benchmark on chr20

Calculate mendelian vialation rate

sudo docker run \
  -v "${PWD}/input":"/input" \
  -v "${PWD}/reference":"/reference" \
  realtimegenomics/rtg-tools format \
  -o /reference/GRCh38_no_alt_analysis_set.sdf "/reference/GRCh38_no_alt_analysis_set.fasta"

FILE="reference/trio.ped"
cat <<EOM >$FILE
#PED format pedigree
#
#fam-id/ind-id/pat-id/mat-id: 0=unknown
#sex: 1=male; 2=female; 0=unknown
#phenotype: -9=missing, 0=missing; 1=unaffected; 2=affected
#
#fam-id ind-id pat-id mat-id sex phen
1 HG002 HG003 HG004 1 0
1 HG003 0 0 1 0
1 HG004 0 0 2 0
EOM

sudo docker run \
-v "${PWD}/input":"/input" \
-v "${PWD}/reference":"/reference" \
-v "${PWD}/output":"/output" \
realtimegenomics/rtg-tools mendelian \
-i "/output/HG002_trio_merged.vcf.gz" \
-o "/output/HG002_trio_annotated.output.vcf.gz" \
--pedigree=/reference/trio.ped \
-t /reference/GRCh38_no_alt_analysis_set.sdf \
| tee output/deepvariant.input_rtg_output.txt

As a result we should get the following output:

Checking: /output/HG002_trio_merged.vcf.gz
Family: [HG003 + HG004] -> [HG002]
35 non-pass records were skipped
Concordance HG002: F:133992/134497 (99.62%)  M:134059/134588 (99.61%)  F+M:132670/133643 (99.27%)
0/137097 (0.00%) records did not conform to expected call ploidy
136009/137097 (99.21%) records were variant in at least 1 family member and checked for Mendelian constraints
2022/136009 (1.49%) records had indeterminate consistency status due to incomplete calls
1058/136009 (0.78%) records contained a violation of Mendelian constraints

Perform analysis with hap.py against 4.2 truth set

mkdir -p happy

sudo docker pull pkrusche/hap.py

sudo docker run \
  -v "${PWD}/benchmark":"/benchmark" \
  -v "${PWD}/input":"/input" \
  -v "${PWD}/output":"/output" \
  -v "${PWD}/reference":"/reference" \
  -v "${PWD}/happy:/happy" \
  pkrusche/hap.py /opt/hap.py/bin/hap.py \
  /benchmark/HG002_GRCh38_1_22_v4.2_benchmark.vcf.gz \
  /output/HG002.output.vcf.gz \
  -f /benchmark/HG002_GRCh38_1_22_v4.2_benchmark.bed \
  -r /reference/GRCh38_no_alt_analysis_set.fasta \
  -o /happy/HG002.output \
  --engine=vcfeval \
  -l chr20

sudo docker run \
  -v "${PWD}/benchmark":"/benchmark" \
  -v "${PWD}/input":"/input" \
  -v "${PWD}/output":"/output" \
  -v "${PWD}/reference":"/reference" \
  -v "${PWD}/happy:/happy" \
  pkrusche/hap.py /opt/hap.py/bin/hap.py \
  /benchmark/HG003_GRCh38_1_22_v4.2_benchmark.vcf.gz \
  /output/HG003.output.vcf.gz \
  -f /benchmark/HG003_GRCh38_1_22_v4.2_benchmark.bed \
  -r /reference/GRCh38_no_alt_analysis_set.fasta \
  -o /happy/HG003.output \
  --engine=vcfeval \
  -l chr20

sudo docker run \
  -v "${PWD}/benchmark":"/benchmark" \
  -v "${PWD}/input":"/input" \
  -v "${PWD}/output":"/output" \
  -v "${PWD}/reference":"/reference" \
  -v "${PWD}/happy:/happy" \
  pkrusche/hap.py /opt/hap.py/bin/hap.py \
  /benchmark/HG004_GRCh38_1_22_v4.2_benchmark.vcf.gz \
  /output/HG004.output.vcf.gz \
  -f /benchmark/HG004_GRCh38_1_22_v4.2_benchmark.bed \
  -r /reference/GRCh38_no_alt_analysis_set.fasta \
  -o /happy/HG004.output \
  --engine=vcfeval \
  -l chr20
Benchmarking Summary for HG002:
  Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  METRIC.Recall  METRIC.Precision  METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
 INDEL    ALL        11256     11208        48        21259        18       9601     11       0.995736          0.998456        0.451620         0.997094                     NaN                     NaN                   1.561710                   2.070802
 INDEL   PASS        11256     11208        48        21259        18       9601     11       0.995736          0.998456        0.451620         0.997094                     NaN                     NaN                   1.561710                   2.070802
   SNP    ALL        71333     71064       269        87357        29      16213      4       0.996229          0.999592        0.185595         0.997908                2.314904                2.053626                   1.715978                   1.712794
   SNP   PASS        71333     71064       269        87357        29      16213      4       0.996229          0.999592        0.185595         0.997908                2.314904                2.053626                   1.715978                   1.712794

Benchmarking Summary for HG003:
  Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  METRIC.Recall  METRIC.Precision  METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
 INDEL    ALL        10634     10582        52        21062        19       9999     14       0.995110          0.998283        0.474741         0.996694                     NaN                     NaN                   1.749861                   2.247423
 INDEL   PASS        10634     10582        52        21062        19       9999     14       0.995110          0.998283        0.474741         0.996694                     NaN                     NaN                   1.749861                   2.247423
   SNP    ALL        70209     69972       237        85198        54      15147     18       0.996624          0.999229        0.177786         0.997925                2.297347                2.069257                   1.884533                   1.874380
   SNP   PASS        70209     69972       237        85198        54      15147     18       0.996624          0.999229        0.177786         0.997925                2.297347                2.069257                   1.884533                   1.874380

Benchmarking Summary for HG004:
  Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  METRIC.Recall  METRIC.Precision  METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
 INDEL    ALL        11036     10985        51        21471        27       9967     17       0.995379          0.997653        0.464208         0.996515                     NaN                     NaN                   1.791542                   2.318601
 INDEL   PASS        11036     10985        51        21471        27       9967     17       0.995379          0.997653        0.464208         0.996515                     NaN                     NaN                   1.791542                   2.318601
   SNP    ALL        71933     71701       232        86303        53      14504     10       0.996775          0.999262        0.168059         0.998017                2.309582                2.071909                   1.878938                   1.772111
   SNP   PASS        71933     71701       232        86303        53      14504     10       0.996775          0.999262        0.168059         0.998017                2.309582                2.071909                   1.878938                   1.772111