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collecting references and annotations --
1. [VarCover: Allele Min-Set Cover Software](https://www.sciencedirect.com/science/article/abs/pii/S1525157819304143)
>To facilitate reference-material s…
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Hello,
I am currently using the MutEnricher program and have encountered an issue with the output results when utilizing my custom GTF files. I created my own GTF files based on both hg19 and hg38 ge…
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Three papers on the TRACERx Renal dataset:
- https://www.cell.com/cell/fulltext/S0092-8674(18)30389-1
- https://www.cell.com/cell/fulltext/S0092-8674(18)30375-1
- https://www.cell.com/cell/fullte…
jjgao updated
2 years ago
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Hello:
Step4.2 is failing to output any variants from scATACseq data. The bam file I am working on belongs to only one cell type. I was able to run the Steps 1 to 4.1 (Skipped step 3 since I was usin…
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I have 13 lung cancer data, some of which are not normal. I hope you can use this software to find somatic mutations.
I ran this program when the following error occurred, I did not understand the re…
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Initial notes on proposed scope and definition of these VA type, based on requirements and considerations documented [here](https://docs.google.com/document/d/1J4AqGDEqyK8KAzfiowgHYKJNvzHuwHSHgkN9dleL…
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_this is a course draft, no dates are fixed yet but this will change soon, comments are welcome_
## Do-Not-Repeat-Yourself
In this 3 parts hacky hours we will learn how to get from raw data to inform…
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Three examples from #360 (originally reported at https://github.com/TranslatorSRI/Babel/issues/333):
* MONDO:0007540 not cliqued with DOID:10017
* MONDO:0017169 not cliqued with DOID:3125
* MONDO:0…
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Hi,
I have been running Palimpsest on mutations in whole genome and same mutations but falling in specific regions of the genome. I observed that in these two different runs, same mutations annotat…
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Hi,
I have a few questions related to the phasing options.
1. Why is the default SNP panel limited to these variants: "7.4M SNPs with minor allele frequency (MAF) > 0.05:"? If I have tumor data …