Jeff S Jasper comments

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                                            Jeff S Jasper

GRCh38 / hg38 stratification BED files

Curious if anyone else has compiled an hg38 resource similar to those found here? Thought I would ask before I jump in to start creating my own and would prefer...

VCF files should be block-gzipped and not gzipped

Hey Brian- Thanks for the nice overview. My use case is meant to be an Rscript run from a command line as part of a workflow. I do need VCFs...

[Request] Replace System.out.print* statements with System.err.print* for stream compatibility

I also would like to see this feature included in ABRA. The ability to pipe the output to sort or deduplication will have a huge increase on performance.

Potential future issue

http://pandas-docs.github.io/pandas-docs-travis/whatsnew In [23]: (df.groupby('A') .agg({'B': {'foo': 'sum'}, 'C': {'bar': 'min'}}) ) FutureWarning: using a dict with renaming is deprecated and will be removed in a future version Out[23]: B C...

Error: no SAMPLE.Chimeric.out.junction file

Hi @personalis - Thanks for reporting the issue. Can you let me know which version of STAR you are using? It looks like STAR changed the behavior of `--chimOutType` on...