Andrew Thrasher

Another example: > SJLGG064626_D1 - CBWD5_locC,CBWD3 chr9 68232051 + intron > 5 127 0.00 0.80 213 0.01 0.05 134 0 25 GTCCTGGCTGAGGAGTGGTTCCAGCAAAGTGGACTCTTCCACGTCCTGCAGCTCCCCCAGTGGCGCCGGATCTAGGAAATATTGTGCCTTTTGCTGAAACTCTGGGGTTGACAGGAGCTCATCTAACAGGCTGGAGGCCCATAGGTGGAAGGGACTTGCCTTGTCTCGGATGAGACTTTGGACTTTGGACTGTGGACTTTTGAGTTAACACTGAAATGAATTAATGCTGAAATGAATTAAGACTTTGGGAGACGGTTGAGA CTX

Thanks @dade7 for the report. @liqingti is looking in to adding this.

Relevant RNApeg results for SJBALL020013_D1 (example from the paper): chrX:1325492:+,chrX:1331449:+ 1 known CRLF2,P2RY8andCRLF2,uc004cpl.1 NM_001012288,P2RY8andCRLF2.1.eAug10,uc004cpl.1 0 0 1 1 0 chrX:1327798:+,chrX:1331449:+ 105 known ENSG00000205755,P2RY8andCRLF2,uc004cpm.1 ENST00000467626,P2RY8andCRLF2.1.dAug10,uc004cpm.1 74 44 61 90 12 chrX:1327801:+,chrX:1331449:+...

Relevant fusion event: P2RY8 chrX 1655814 - 5utr CRLF2 chrX 1331529 - coding > 28 28 255 211

Other fusions that may be relevant TAL1-STIL. Internal deletions in PAX5 and CTNNB1 (exon 3).

> @adthrasher can you split the `samtools.wdl` changes off into a stand-alone PR? I think those changes are good and should be merged. They don't have to wait on the...

@claymcleod - I don't think you need to review the Arriba changes, but I wanted to ping you for the STAR changes. I'm opting to change some parameters here to...

@a-frantz - I rebased from `main`. So this should contain all of the parameter renames. I've updated them in `rnaseq-core` as well. I think I've got it all clean now....

Hi Dennis, You may want to check out [`ngs generate`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-generate). @claymcleod wrote the tool and it can generate `fastq` files from one or more reference genomes.

I can read the naming convention. That doesn't change that the compiler should simply report which element it is processing when it encounters the issue, rather than dumping a stack...