Simon C Chu

It seems the program hang there. Sometimes the output from the third program (here wtpoa-cns) may block the pipe and cause issue like this. I don't have a good solution...

@adriludwig , use "-y 32". Here is a readme: https://github.com/parklab/xTea/tree/master/xtea/rep_lib_prep (at the bottom). It's not convenient as you can only run one repeat type at a time. I'll try to...

@dongjuleem yes, you can use that one, which just misses the gene annotation and field annotation.

@dongjuleem The main difference is internally the somatic module use lower cutoff (considering the tumor purity, as well as false positives could be further filtered out when checking the ctrl...

I directly use the somatic mode for my research, but it depends on your specific requirements.

I'll add the support in the coming few weeks.

I have this script to merge vcfs to one: https://github.com/parklab/xTea/blob/master/xtea/x_vcf_merger.py, but it's not like the standard "genotyping" module, and just merge the vcfs. You can also do this using other...