Implement trio/multi
Closed this issue · 9 comments
marc-sturm commented
Implement trio/multi
leonschuetz commented
Sniffles has trio mode: link
- implement
- adapt annotation
- test
leonschuetz commented
Clair3 has a trio version: Clair3-Trio
- [ ] test
- [ ] implement
rejected do to long runtime
leonschuetz commented
test data:
- S:\projects\research\21073N_SEQ418081722_trio\Sample_21073LRa013 - Sample_21073LRa015
leonschuetz commented
Clair3 first results:
- takes very long (aborted after 5 Days with 4 threads)
- very high memory usage
-
test new version with memory leak fix (not available via docker yet)
leonschuetz commented
Test with GATK combineGVCF
leonschuetz commented
First test seems to work:
- implement php script to use
- add genotype calling
- add post-processing
- add multithreading
- implement in pipeline
leonschuetz commented
- implement pipline tests
- trio
- multi
- validate
- integrate in GSvar
leonschuetz commented
- run trios/multis from Joo
leonschuetz commented
- fix bug in
merge_gvcf.php