tamsen

Hi, No, tech support isnt wrong, per se. Its just that there are many filters at many levels. All reads used by Pisces are filtered _before_ variant calling takes place,...

There will be various levels of filtering, and read stitching, and for some types of variants (such as indels) AD is calculated a bit differently than total DP, so any...

Hi there, I have your email. I will contact you!

Hi, Sorry for the late response. So, the contigs in your genome size .xml file are just numbers, as in "1" , see below: fileName="Homo_sapiens.GRCh38.dna.primary_assembly.fa" contigName="1" And the contigs named...

Yeah, that's not expected. Whats your command line? Was this BAM produced by the stitcher, and was the same Pisces version used for the Stitcher and for Pisces? What version...

I'm glad you found a work around. But I'm not happy about the behavior. We'll get back to you on this.

Hi there, I'm afraid this issue is lingering at the bottom of our backlog. It wont be fixed till 5.2.11, at least. If either of you have any small sample...

I didn't personally set any of the Pisces/conda integration up, but presumably b/c that is the latest release on the fork conda is tracking. 5.2.10.49 is the most recent official...

I recommend my fork. Should be much more friendly and stable for HPC and Linux.

Hi, Yes, absolutely! It should be fine. If you are going to look for variants that are less that 1% of the sample mixture, you will not want the default...