Simon C Chu

Could you use the git cloned version (`git clone https://github.com/parklab/xTea`) rather than the bioconda version and have a try again？(don't forget the reset --xtea)

You activate your conda environment (suppose this is how you install following the docker file), then git cloned xtea (git clone https://github.com/parklab/xTea) to a folder say: `/n/path/xTea`. Then, you run...

This one is fine. You can ignore. Have you gotten the vcf file?

Hi, case-ctrl mode is used to identify somatic TE insertions. We don't expect a genotype information for somatic insertions. We classify germline ones to heterozygous or homozygous to indicate they...

If this is the case, then it's a false positive. Just not sure why this is reported, since the signal in control is strong.