Omega Alpha

BR: HMMRATAC throws an exception when using samblaster-deduped bam file even with --removeDuplicates false

1

**To Reproduce** the bam file has been sorted by `samtools sort` and deduplicated by `samblaster`. **Screenshots** **System (please complete the following information):** - OS: centos7 - JRE version: openJDK 8...

Enhancing outputs compatibility

1

It seems like the MiXCR outputs, especially for .vdjca and .clnx files, do not fit the MiXCR program. For example, I ran alignment using the MiXCR 4.0 release downloaded from...

A bug like code injection if prefix name contains underline

1

for example, if we use `-n HiC_K562` as prefix name. The string parsers may get wrong results. like ~~~ chrompair = paste(strsplit(matrix,'_')[[1]][2],strsplit(matrix,'_')[[1]][3],sep="_") ~~~ in externalScripts/getBreakPoints2steps.R

Seeking for the BEST practice of splitting CRAM file

1

I have developed a bioinformatics pipeline that processes alignment results generated by minimap2, with an emphasis on minimizing the disk storage and maximizing analysis speed. To achieve this, I opted...