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I’m new to working with computers tools like DeepVariant. I’m trying to build DeepVariant using Docker on a Mac M1 and am encountering issues with the Dockerfile during the Bazel build process. I want…
ghost updated
2 months ago
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**Hello, I ran deep variant for mutation calling of single cell iso seq bam file (Pacbio long read rna-seq), and I got this error messages:**
`9-03 12:26:09.055921: W third_party/nucleus/io/sam_reade…
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Hi,
Why all the GT of the PASS variant site is 1/1? use deepsomatic.
chr1 91748 . C T 10 PASS . GT:GQ:DP:AD:VAF:PL 1/1:10:61:48,13:0.213115:9,19,0
The command:
BIN_VERSION="1.6.1"
docker…
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Hi,
I see the vcf is generated from deepvariant.
Is it more reasonable to use deepsomatic to call snv in tumors, as opposed to using deepvariant?
I am confused about the choice of vcf, shoul…
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Hi,
How to filter variant sites after running deepsomatic. Is it enough to extract only the variant sites marked as 'PASS' in the FILTER column of the VCF file?
What are the recommended methods…
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Hi,
Why all the GT of the PASS variant site is 1/1? use deepsomatic.
chr1 91748 . C T 10 PASS . GT:GQ:DP:AD:VAF:PL 1/1:10:61:48,13:0.213115:9,19,0
The command:
BIN_VERSION="1.6.1"
docker …
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Hi,
Why all the GT of the PASS variant site is 1/1? use deepsomatic.
chr1 91748 . C T 10 PASS . GT:GQ:DP:AD:VAF:PL 1/1:10:61:48,13:0.213115:9,19,0
Best wishes.
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This is from DeepVariant's documentation.
"For somatic data or any other samples where the genotypes go beyond two copies of DNA, DeepVariant will not work out of the box because the only genotypes…
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Hi,
First of all, thank you for open sourcing DeepSomatic. Hope that it is going to be a useful tool for the community moving forward.
I am unable to reproduce the variant calling performance re…
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hello, i saw a comment from 2022 that this was not developed, i wonder if you are moving towards this
thanks
christos