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## Background
VMC currently uses [Identifier](https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.kj21ornkb4u7) objects that consist of a `namespace` and…
reece updated
5 years ago
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Dear Salmon team,
I am trying to quantify allele specific expression using salmon, so I would like to use the unique counts to estimate confidence itervals of the allele unbalance. However, I get n…
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Dear Dr. Dobin,
In quantifying allele-specific-expression, I am using STAR to map reads against a diploid genome (custom concatenated fasta files for each race and same for annotation). In the coun…
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I got a general out of index error in step2_export_to_elasticsearch as below,
Caused by: java.lang.IndexOutOfBoundsException: 0
File "/opt/seqr/hail-elasticsearch-pipelines/hail_scripts/v01/utils/e…
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I have successfully annotated my vcf file using a local installation of variant effect predictor (VEP). However, the filtering doesn't work. E.g. the command
`filter_vep -i vep.test.vcf.gz -filter …
matmu updated
5 years ago
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Hi -- I was able to successfully run CharGer, but all variants are classified as "Uncertain Significance." Is there a setting that must be tweaked for variant annotation to work correctly? I'm guessin…
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Hi Brent,
Thanks again for wonderful tool.
I was trying to use this part.
"recessive:recessive_func(kid, mom, dad)"
and I am getting some error. I am just wondering if I have to load this rec…
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3. core_tight
```
> head(core_tight)
study_accession study_title
1 SRP012682 Genotype-Tissue Expression (GTEx) Common Fund Project
2 SRP0…
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@dancooke
possible label for that issue:Question
Hi Daniel,
In the 0.4.1-alpha Octopus' VCF, there are several fields listed in the vcf header for FILTER, INFO and FORMAT columns.
I am inte…
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Dear Bcbio Team,
I upgraded bcbio recently to v1.1.5 and I am getting below error when running gatk-variant pipeline.
[April 28, 2019 10:11:25 AM AST] org.broadinstitute.hellbender.tools.spark.A…