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I ran GATK 4.1.0.0 Mutect2 on a small (~1Mb) targeted panel. I am using a normal control that is not the same individual (basically to exclude technical artifacts), so I do expect to see more variants…
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Hi Sierra team,
I am trying to calculate the peak matrix from scRNA-seq data from human tumor. The vignettes goes well. But I get some problems when annotating peak. Reference genome and gtf file w…
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Hello,
I'm running into an error with mutect2 (`java.lang.IllegalArgumentException: log10 p: Values must be non-infinite and non-NAN`) when using a pair of FASTQ files with yeast sequence reads. Ot…
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This is a very useful tool! Thanks for developing.
I have a question. I want to use the tool to identify the normal cells from single cells by using the infercnv. There are lots of output files.Whi…
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GIven the interest in studies that involve tumor heterogeneity / subclonality, currently bcbio offers "out of the box" support for both somatic variants and CNVs. A useful metric that can be combined …
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Hi,
I can get InferCNV to run OK locally on the sample data, but the run fails as follows when I run it on my own data (derived from 10x 3' data, in case that's relevant):
```
STEP 13: Run Bayesi…
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MuTect and VarScan has a threshold setting (`--tumor_f_pretest`) to select sites with at least a certain fraction of non-REF alleles. Something similar is in VarScan (minimum frequency to call an alle…
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I am running delly2 current version on multiple tumor-normal pairs. For one of the pairs, it is taking a lot longer than the rest (5 days now). Looking at the output it is still stuck in the split rea…
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https://github.com/tgen/phoenix/blob/657be197a850300980b8b5e4e5cd9586981284d9/modules/somatic/octopus.jst#L14
It looks like we are still using 0.6.0 when the AD and AF updates were in 0.6.1 and now…
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You can execute Picard AddOrReplaceReadGroups tool without setting Platform Unit (PU), however setting PU is required and results in a runtime error:
```
ERROR: Option 'RGPU' is required.
USAGE: …