我正在尝试在我的 BAM 文件上运行 DeepVariant 以生成 VCF。我有以下问题:
1 - 对齐在 GRCh38 中,我应该使用哪个模型。我可以使用标准的全外显子组序列模型吗?('gs://deepvariant/models/DeepVariant/0.7.0/DeepVariant-inception_v3-0.7.0+data-wes_standard')
2 - 使用哪个 BED 文件来指定外显子组区域?有标准的吗?我在这里找到了一个我现在正在使用的(“CDS-cannonical.bed”): https ://github.com/AstraZeneca-NGS/reference_data/tree/master/hg38/bed
3 - 我使用的是 Verily GRCh38 基因组,谷歌基因组学上是否有标准的 GRCh38 比对。这是我拥有的:--ref gs://genomics-public-data/references/GRCh38_Verily/GRCh38_Verily_v1.genome.fa \
我的脚本设置如下,如果有意义,请告诉我:
#!/bin/bash
set -euo pipefail
# Set common settings.
PROJECT_ID=valis-194104
OUTPUT_BUCKET=gs://canis/CNR-data
STAGING_FOLDER_NAME=deep_variant_files
OUTPUT_FILE_NAME=TLE_a_001.vcf
# Model for calling whole exome sequencing data.
MODEL=gs://deepvariant/models/DeepVariant/0.7.0/DeepVariant-inception_v3-0.7.0+data-wes_standard
IMAGE_VERSION=0.7.0
DOCKER_IMAGE=gcr.io/deepvariant-docker/deepvariant:"${IMAGE_VERSION}"
COMMAND="/opt/deepvariant_runner/bin/gcp_deepvariant_runner \
--project ${PROJECT_ID} \
--zones us-west1-b \
--docker_image ${DOCKER_IMAGE} \
--outfile ${OUTPUT_BUCKET}/${OUTPUT_FILE_NAME} \
--staging ${OUTPUT_BUCKET}/${STAGING_FOLDER_NAME} \
--model ${MODEL} \
--regions gs://canis/CNR-data/CDS-canonical.bed \
--bam gs://canis/CNR-data/TLE_a_001_R_2014_09_17_16_35_30_user_WAL-19-TLE_17_09_2014_Auto_user_WAL-19-TLE_17_09_2014_57.bam \
--ref gs://genomics-public-data/references/GRCh38_Verily/GRCh38_Verily_v1.genome.fa \
--gcsfuse"
# Run the pipeline.
gcloud alpha genomics pipelines run \
--project "${PROJECT_ID}" \
--service-account-scopes="https://www.googleapis.com/auth/cloud-platform" \
--logging "${OUTPUT_BUCKET}/${STAGING_FOLDER_NAME}/runner_logs_$(date +%Y%m%d_%H%M%S).log" \
--zones us-west1-b \
--docker-image gcr.io/deepvariant-docker/deepvariant_runner:"${IMAGE_VERSION}" \
--command-line "${COMMAND}"
编辑:
我尝试添加使用 samtools 生成的 .bam.bai 文件(bam 索引)
我仍然收到一个错误:
Traceback (most recent call last):
File "/opt/deepvariant_runner/src/gcp_deepvariant_runner.py", line 862, in <module>
run()
File "/opt/deepvariant_runner/src/gcp_deepvariant_runner.py", line 845, in run
_run_make_examples(pipeline_args)
File "/opt/deepvariant_runner/src/gcp_deepvariant_runner.py", line 340, in _run_make_examples
_wait_for_results(threads, results)
File "/opt/deepvariant_runner/src/gcp_deepvariant_runner.py", line 352, in _wait_for_results
result.get()
File "/usr/lib/python2.7/multiprocessing/pool.py", line 572, in get
raise self._value
RuntimeError: Job failed with error "run": operation "projects/valis-194104/operations/13939489157244551677" failed: executing pipeline: Execution failed: action 5: unexpected exit status 1 was not ignored (reason: FAILED_PRECONDITION)
details: