In this case study, we show an example of running DeepSomatic on FFPE WGS data. We use HCC1395 as an example for this case study.
For this case-study, we use HCC1395 as an example. We run the analysis on chr1
that we hold out during training.
Please see the metrics page for details on runtime and data.
Docker will be used to run DeepSomatic and hap.py,
We will be using GRCh38 for this case study.
BASE="${HOME}/deepsomatic-ffpe-wgs-case-study"
# Set up input and output directory data
INPUT_DIR="${BASE}/input/data"
OUTPUT_DIR="${BASE}/output"
## Create local directory structure
mkdir -p "${INPUT_DIR}"
mkdir -p "${OUTPUT_DIR}"
mkdir -p "${OUTPUT_DIR}/sompy_output"
# Download bam files to input directory
HTTPDIR=https://storage.googleapis.com/deepvariant/deepsomatic-case-studies/deepsomatic-chr1-case-studies
# Download the reference files
curl ${HTTPDIR}/GCA_000001405.15_GRCh38_no_alt_analysis_set.chr1.fna > ${INPUT_DIR}/GCA_000001405.15_GRCh38_no_alt_analysis_set.chr1.fna
curl ${HTTPDIR}/GCA_000001405.15_GRCh38_no_alt_analysis_set.chr1.fna.fai > ${INPUT_DIR}/GCA_000001405.15_GRCh38_no_alt_analysis_set.chr1.fna.fai
# Download the bam files
curl ${HTTPDIR}/HCC1395_ffpe_wgs.normal.chr1.bam > ${INPUT_DIR}/HCC1395_ffpe_wgs.normal.chr1.bam
curl ${HTTPDIR}/HCC1395_ffpe_wgs.normal.chr1.bam.bai > ${INPUT_DIR}/HCC1395_ffpe_wgs.normal.chr1.bam.bai
curl ${HTTPDIR}/HCC1395_ffpe_wgs.tumor.chr1.bam > ${INPUT_DIR}/HCC1395_ffpe_wgs.tumor.chr1.bam
curl ${HTTPDIR}/HCC1395_ffpe_wgs.tumor.chr1.bam.bai > ${INPUT_DIR}/HCC1395_ffpe_wgs.tumor.chr1.bam.bai
# Download truth VCF
DATA_HTTP_DIR=https://storage.googleapis.com/deepvariant/deepsomatic-case-studies/SEQC2-S1395-truth
wget -P ${INPUT_DIR} "${DATA_HTTP_DIR}"/High-Confidence_Regions_v1.2.bed
wget -P ${INPUT_DIR} "${DATA_HTTP_DIR}"/high-confidence_sINDEL_sSNV_in_HC_regions_v1.2.1.merged.vcf.gz
wget -P ${INPUT_DIR} "${DATA_HTTP_DIR}"/high-confidence_sINDEL_sSNV_in_HC_regions_v1.2.1.merged.vcf.gz.tbi
DeepVariant pipeline consists of 3 steps: make_examples_somatic
, call_variants
, and
postprocess_variants
. You can run DeepSomatic with one command using the
run_deepvariant
script.
BIN_VERSION="1.8.0"
sudo docker pull google/deepsomatic:"${BIN_VERSION}"
sudo docker run \
-v ${INPUT_DIR}:${INPUT_DIR} \
-v ${OUTPUT_DIR}:${OUTPUT_DIR} \
google/deepsomatic:"${BIN_VERSION}" \
run_deepsomatic \
--model_type=FFPE_WGS \
--ref=${INPUT_DIR}/GCA_000001405.15_GRCh38_no_alt_analysis_set.chr1.fna \
--reads_normal=${INPUT_DIR}/HCC1395_ffpe_wgs.normal.chr1.bam \
--reads_tumor=${INPUT_DIR}/HCC1395_ffpe_wgs.tumor.chr1.bam \
--output_vcf=${OUTPUT_DIR}/HCC1395_deepsomatic_output.vcf.gz \
--sample_name_tumor="HCC1395Tumor" \
--sample_name_normal="HCC1395Normal" \
--num_shards=$(nproc) \
--logging_dir=${OUTPUT_DIR}/logs \
--intermediate_results_dir=${OUTPUT_DIR}/intermediate_results_dir \
--regions=chr1
NOTE: If you want to run each of the steps separately, add --dry_run=true
to the command above to figure out what flags you need in each step. Based on
the different model types, different flags are needed in the make_examples
step.
--intermediate_results_dir
flag is optional. By specifying it, the
intermediate outputs of make_examples_somatic
and call_variants
stages can be found in the directory.
sudo docker pull pkrusche/hap.py:latest
# Run hap.py
sudo docker run \
-v ${INPUT_DIR}:${INPUT_DIR} -v ${OUTPUT_DIR}:${OUTPUT_DIR} \
pkrusche/hap.py:latest \
/opt/hap.py/bin/som.py \
-N ${INPUT_DIR}/high-confidence_sINDEL_sSNV_in_HC_regions_v1.2.1.merged.vcf.gz \
${OUTPUT_DIR}/HCC1395_deepsomatic_output.vcf.gz \
-r ${INPUT_DIR}/GCA_000001405.15_GRCh38_no_alt_analysis_set.chr1.fna \
-o ${OUTPUT_DIR}/sompy_output/deepsomatic.chr1.sompy.output \
--feature-table generic \
-R ${INPUT_DIR}/High-Confidence_Regions_v1.2.bed \
-l chr1
The output:
type total.truth total.query tp fp fn unk ambi recall recall_lower recall_upper recall2 precision precision_lower precision_upper na ambiguous fp.region.size fp.rate
0 indels 133 132 106 26 27 0 0 0.796992 0.722688 0.858537 0.796992 0.803030 0.729050 0.863894 0 0 248956422 0.104436
1 SNVs 3440 3001 2835 166 605 0 0 0.824128 0.811136 0.836575 0.824128 0.944685 0.936075 0.952439 0 0 248956422 0.666783
5 records 3573 3133 2941 192 632 0 0 0.823118 0.810347 0.835365 0.823118 0.938717 0.929911 0.946713 0 0 248956422 0.771219