Brendan

FWIW, sounds like there's an official end-of-life for python 2 in just a few months: https://www.python.org/doc/sunset-python-2 . Just something to be aware of as you consider future plans for Manta

Any word on this? Seems like an important feature, BED is the format used by (I think) every other CNV caller, would be a shame not to support it.

Thanks! I just tried that, but it's still not finding any supplementary hits for some of these reads, compared to BWA, at least). The reads do have a bunch of...

Hi again, I tried adding "--mapping-mode=sensitive" (and retaining -M 100), but I'm still not seeing any reads with the "supplementary" (0x800) flag set, or that have the SA tag, for...

Thanks for looking into this, I'm aligning to the human genome reference (hg19), here's an example of a read pair that BWA thinks should have a supplementary hit, but doesn't...

Yes, you're totally right, maybe that wasn't the greatest example. Below I pasted a read pair for which the XA tag isn't present at all. But the important point isn't...

Thanks again for your help with this! So is it correct to say that GEM doesn't emit reads with the SA tag or supplementary bit set, but instead encodes the...

Sorry for the delayed response, but looks like the issue still persists even with double quotes $ CoNVaDING.pl -mode StartWithBestScore \ -inputDir match_controls \ -outputDir final_calls.nominal.defaults \ -ratioCutOffLow "0.65" \...