tamsen

Hi, Have you tried moving libFileCompression.so into your exe folder? You should find it in src/AdditionalFilesForLinux/libFileCompression.so

re CompressionLib issue: Hm, I typically use on Linux, CentOS 6.8. What are your system specs? I can try to reproduce. This is how I submit to our cluster: >...

Follow up: We have heard of people having problems with libFileCompression.so in systems with very old zlib versions that don't support the recent API (and by recent I mean v1.2.3,...

Hi Rosemarie. Thanks for your continued interest. Sorry, we do not natively handle UMIs with Pisces. To keep the software clean, architecturally, it is a deliberate choice to handle UMIs...

OK, here we go. An example UMI bam-collapsing app that works well with Pisces, for finding low freq variants at fractions of a percent. https://basespace.illumina.com/apps/5528523/UMI-Error-Correction?preferredversion

Hi! Looks like a bug! Thanks for submitting the bug report. We are currently working on hardening Gemini, so we really appreciate hearing about any issues you find. This might...

Hi :) Yes, its certainly both a bug and an unhandled exception. Is the bam something you could send us? short answer: Yes, its a bit odd to see Gwenn's...

Hi! Sorry for your frustration. Go ahead and try this 5.3 version. It resolves some gemini stability issues. https://github.com/tamsen/Pisces/releases/tag/v5.3.0.0 Make sure you see the readme for the command line changes...

"--collapse" will change the called variants, generally filtering out noise cause by variants broken up by read boundaries.. The idea is that variants that span multiple bases can run off...

Also, this might be helpful. https://github.com/Illumina/Pisces/wiki/Pisces-5.2.10-Supported-Options