Fritz Sedlazeck

So the --non-germline is for mosaic , low variant frequency mutations. They could be of interested for cancer. We are currently running benchmarks to see if it is better to...

You mean after the merge right ? Yes that is the easiest way... although there is a bit of a catch. So if a variant is too low in read...

Hi Ayush, just to be sure that is on the population level right ? Not on the single sample calling ? Thanks Fritz

Thanks everyone. I am traveling but will try that and Minimac4 for these files. Thanks Fritz

Ok I am sorry guys this is a very nooby question and its not necessarily related to emeraLD. So I have this VCF file with just called SNPs of multiple...

Hi, the merge combines two overlapping SV to one entry and notes the merge in the GT fileds. Can you post a part of the VCF file? This is a...

Dear @biozzq , no SURVIVOR does not take the GT into account as many tools often dont report the GT. The example you show here is such a case. You...

Dear @hygine , thanks for sending the sample. @1: Seems to work for me. Maybe try to pull the newest code version and try again: `15 25612378 7916 N ....

Dear @biozzq We typically dont do genotyping often. There are tools that you can use but most of them are quite optimized for their own SV Caller: https://academic.oup.com/gigascience/article/8/9/giz110/5565134 We recently...

What was your parameter? If you put in 1000 for the distance than this result is fine. The start and stop are within 1000bp of each other. The resulting entry...