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weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
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LOCO with bgen chunk files (not split by chromosome) #334

Closed sboer closed 2 years ago

sboer commented 3 years ago

Hi! I was wondering whether it is possible to run analysis with LOCO = TRUE, using bgen files, split in chunks (with each file/chunk containing several chromosomes)? Could not find anything in the manual or --help function. Tried both not to specify --CHR, and to specify several chr (according to the file analysed) but nothing seemed to work.

Thanks!

Sigrid

weizhouUMICH commented 3 years ago

Hi Sigrid,

The LOCO=TRUE currently only works with bgen or vcf files containing a single chromosome. The reason for this setting is to avoid checking the chromosome for each testing marker, which can cost much time.

Thanks, Wei

sboer commented 3 years ago

Good to know, thanks Wei :)

Sigrid

weizhouUMICH commented 2 years ago

We have just released a new version 1.0.0. It has substantial computational efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests and clearer log output. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIGE-doc/ The program will be maintained by multiple SAIGE developers there. The docker image has been updated. Please feel free to try the version 1.0.0 and report issues if any.

Thanks! Wei