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I've successfully run the example. I don't understand the output
out/merged_snp/jurkat_chr1/final.tsv.gz
What is the final call? And is what should I use as the measure of confidence?
Thank…
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It seems that the ALT field being produce by `write_vcf()` is an integer. The VCF v4.2 spec indicates that the ALT field should be a nucleotide, a star, or a symbolic allele in angle brackets. The VCF…
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Annotations to anatomy term P6.p are problematic because when computed on, one cannot arrive at it's vulval or non-vulval nature; Annotations need to be changed to either 'P6.p hermaphrodite' or 'P6.p…
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### Submitter Name
Martin Maiers
### Submitter Affiliation
National Marrow Donor Program
### Submitter Github Handle
mmaiers_nmdp
### Additional Submitter Details
_No response_
### Which event…
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Hi,
I've been using your tool to identify CNVs in 10x Genomics scRNA-seq data. However, I have one question regarding the filtering of identified CNVs. When I run the calcAlleleCnvProb function on…
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Hi,
I've run MMSeq on my samples. For only a few of them MMSeq output the .mmseq files. But for most of them these outputs (*.mmseq, *.genes.mmseq, and *.identical.mmseq) are missing while the *_gi…
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For pathogens and host genotypes, many natural variants occur and for these, we want to capture the differences to some nominally WT variant. We need to be able to distinguish when a variant is na…
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Dear Stephane,
pHASER has been quite helpful for me. However, I'm trying to assess allele-specific gene expression in single-cell RNA-Seq data from human lung cancer cells and I have tried it many ti…
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What functionalities are available in JacusaHelper for looking at RRD data? The documentation says that AddBaseChangeInfo, AddEditingFrequencyInfo, etc. are only applicable for RDD data. Why is this t…
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The following syntax ambiguities/parsing issues remain in the draft VCF 4.3 specs:
#### Non-printable ASCII characters:
- U+0000 causes causes paring issue for C implementations
- Allowing alternate l…