Read several biostars posts:
Best Genome Browser To Look At Structural Variation Calls
Which Multiscale Genome Browser Is The Best At Visualizing Structural Variants?
Use svviz
For some background on ssh tunnelling:
In HPC nautilus:
svviz -p 7777 -t del -b my.bam Homo_sapiens_assembly19.fasta 1 29320981 29321462
svviz -p 7777 -t ins -b my.bam Homo_sapiens_assembly19.fasta 3 2516030 2516054
####translocation
svviz -p 7777 -t tra -b my.bam Homo_sapiens_assembly19.fasta 7 50996890 9 106346679 +
start an ssh tunnel to the server on my own computer:
ssh -L 127.0.0.1:7777:127.0.0.1:7777 username@nautilus -N
open 127.0.0.1:7777 on my local computer.
Use pybamview
In HPC:
pybamview --port=7777 --bam my.bam --ref Homo_sapiens_assembly19.fasta
on my own computer:
ssh -L 127.0.0.1:7777:127.0.0.1:7777 mtang1@nautilus -N
####Another way to do it:
on HPC:
hostname -f
cnode338.mdanderson.edu
Use the option "--ip 0.0.0.0", which will allow a remote user to view the results. Also set which port to serve the web application by setting "--port $PORT" where $PORTis some large number, between 1024-65535. This must be a port for which your server's security settings allow incoming http traffic. The default port for PyBamView is 5000. An example command is shown below:
pybamview --ip 0.0.0.0 --port=7777 --bam my.bam --ref Homo_sapiens_assembly19.fasta
pybamview --ip 0.0.0.0 --port=7777 --bam mt.bam --ref Homo_sapiens_assembly19.fasta
Navigate to http://$HOSTNAME:$PORT in a web broswer, where $HOSTNAME is the hostname mentioned above, and $PORT is the argument you used for the port. You can share this URL, or navigate to an interesting alignment view and copy the resulting URL from the browser, with another person that has access to the same server. Note that if you need VPN to access the server, the other user will probably also need VPN access to view the URL.
for example:
http://cnode338.mdanderson.edu:7777
ssh -Y hostname
see github page I will investigate a bit on it.