[input file ] smrtsv.py detect parameter

EichlerLab / smrtsv2

Structural variant caller

MIT License

53 stars 6 forks source link

[input file ] smrtsv.py detect parameter #23

Closed Xuelei-Dai closed 5 years ago

Xuelei-Dai commented 5 years ago

Hi Peter I have stuck in detecting SV using your software smrtsv2. The README is quite ambiguous, especially the input file parameter. I am wondering how could I input a bam file with detect command. And could you please providing me any detailed handbook about how to run correctly in every step. Thanks in advance.

paudano commented 5 years ago

In README.md, search for "To run all steps:".

You don't need to run each step individually. You don't input a BAM into "detect". It is input into "align", and detect gets what it needs from the "align" output. Just use the "run" command, it does everything.