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Strange GT value #592

@li1ba

Description

@li1ba

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.

igv_panel_chr2_24146804

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.

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