singerj

Hi, We will include a working example for WGS data, however, this will take some time. In the meantime, the WES example can be used for variant calling. If applied...

Hi, Sorry for the late response. I am trying to reproduce the error you encounter. In the meantime you can try to install SCIPhI using cmake. In addition, I am...

Hi, Thanks for reporting this problem. I have not experienced this before. I am going to have a look and remove any "using namespace std" to make these things more...

Hi, Sorry for the delay. The bioconda packaging takes a little longer as expected since bioconda just switched to a new version of the build system.

Dear Tamara, The problem is that during candidate loci identification not a single locus is determined as likely harbouring a mutation. I will include a check and omit the phylogenetic...

Also note that the "-r" option was removed in the current version as intermediate results are not stored. Instead SCIPhI should be invoked several times with different seeds.

Dear Tamara, The "-u" is not the problem, which is used to decide which mutations to include into the final VCF. Could you paste the content of the "SciphiSamples.${PATIENT}.txt" file?