Frank Austin Nothaft
Frank Austin Nothaft
@jstjohn oh, hah! Goofy mistake on my side. I think that is an easy change to make, actually! I will have a PR against this branch with the fix tomorrow.
Hi @shibuvp! Sorry for the confusion, docs are a bit out of date. Avocado needs to be built for Spark 2, due to a bug in Spark SQL in Spark...
No problem! Please leave this issue open; it'll remind me to update the docs.
Sure, can do. What genome build are you on?
Does your reference build have "chr" suffixes on the chromosome names?
OK, interesting. BTW, what is the approximate coverage of your file?
The aligned reads or FASTQ.
That error is expected on Spark 1.6.2. Can you run `./scripts/move_to_spark2.sh` and rebuild? No worries about the coverage. I'll pull together some default parameters for you in a sec.
https://gist.github.com/fnothaft/627f4e295f9400cff453b6c3f671fd7d should be a reasonable set of default parameters. Let me know if you run into any problems!
Yup, ADAM and SAM/BAM/CRAM are both fine.