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Description
Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.4/docs/FAQ.md: Yes
Describe the issue:
(A clear and concise description of what the issue is.)
A variant with VAF value 1 is called as heterozygous. The IGV visualisation of the .bam file shows that it should clearly be a homozygous variant.
Here the line from .vcf file:
chr2 24146804 . C T 29.5 PASS . GT:GQ:DP:AD:VAF:PL 0/1:3:162:0,162:1:26,0,0
.gvcf file:
chr2 24146804 . C T,<*> 29.5 PASS . GT:GQ:DP:AD:VAF:PL 0/1:3:162:0,162,0:1,0:26,0,0,990,990,990
We also asked our collaborators to run the same sample and in their results, a homozygous variant is called:
chr2 24146804 . C T 30.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:5:161:0,161:1:28,2,0
chr2 24146804 . C T,<*> 30.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:5:161:0,161,0:1,0:28,2,0,990,990,990
What could cause this discrepancy, if the DeepVariant versions and commands are the same?
Setup
- Operating system: Ubuntu16.04
- DeepVariant version: 1.2.0
- Installation method (Docker, built from source, etc.): Docker
- Type of data: (sequencing instrument, reference genome, anything special that is unlike the case studies?)
NovaSeq 6000 using Twist Comprehensive Exome with mtDNA add-in, GRCh38
Steps to reproduce:
- Command:
docker run \
-v ${MOUNT_DIR}:${MOUNT_DIR} \
google/deepvariant:1.2.0-rc0 \
/opt/deepvariant/bin/run_deepvariant \
--model_type=WES \
--ref="${REFERENCE}" \
--reads="${INPUT}" \
--regions="${CAPTURE_KIT}" \
--output_vcf=${OUTPUT_VCF} \
--output_gvcf=${OUTPUT_GVCF} \
--num_shards=64 \
--postprocess_variants_extra_args="only_keep_pass=true"
- Error trace: (if applicable)
Does the quick start test work on your system?
Please test with https://github.com/google/deepvariant/blob/r0.10/docs/deepvariant-quick-start.md.
Is there any way to reproduce the issue by using the quick start?
No.