Zev Kronenberg
Zev Kronenberg
Hi @djakubosky, Thanks for reaching out, these are really good questions, especially for large cohorts. I've made some bullet points that might help guide you. If you find this helpful...
@djakubosky, Yes mergeSV can be used to merge within, and then between. You mentioned that you have families in your cohort? I'd joint call closely related individuals (up to 3/4)....
Hello @Addicted-to-coding, I'd be happy to help you trouble shoot. First, what happens if you don't pipe the whamg stdout to the filtering script? Do you get any SV calls?...
What is printed to STDERR and STDOUT?
What aligner did you use? Is this exome or whole genome data? I'd expect at least a couple SVs for WGS data.
Hi @mwalker174, I've marked this as a question, but it's possible it is a bug. Let me think about this for a bit.
Can you provide an example and what you'd like to see?
Hi @mpauper, What system are you using? Do you have a newer version of bamtools in your path?
Hi Shawn, Did you try updating the checkout of bamtools prior to the build, like I suggested? Did that solve the problem? If so, I will just update the bamtools...
@abolia Thank you. I'm trying them out now.