jiyue1214

Nextflow pipeline is running on Slurm and can be monitored by the nextflow tower daily. Question: @karatugo, According to the scrontab, we have not activated the refresh harmonisation queue, queue...

We have migrated all crontab jobs to Slurm this morning. This ticket can be moved to Done. Just need to double-check if they are running successfully tomorrow.

Genome-wide sequencing: | | GWAS_id | Techniques | harmonised | Raw_rows | Harmonised_rows | hm_14 | hm_15 | hm_16 | Drop_ration | hm_15(%) | | - | ------------ | ----------------------...

Next to do: 1. GCST90010173, and GCST90161593: explore the reason why ~20% variants are dropped in the harmonised file. 2. Run harmonisation against the new ensemble version as well. 3....

1. Reason why variants are dropped - GCST90010173: contains lots of variants that reference allele=alternative allele ~ 10.5%; ~14% variants cannot find VCF records - GCST90161593: 5% variants cannot find...

For variants that can be harmonised by V_95 but not V_111, it happens to two conditions: 1. Some indels: variants representation in V_95 and V_111 are 1-base shift. These VCF...

@ljwh2 Can we close this ticket? After our investigation: 1. There were only 5 whole genome sequencing data. 2. The rate of harmonization among these five studies varies widely, ranging...

The harmonised result is available on the FTP right now and could @karatugo double-check if the data is correct?

Feedbacks: - [x] Show if the file is selected successfully - [x] Instructions/documentation on how to edit the configure file - [ ] Step 3 is too long to read...

I have created pre-defined configuration for the BLOT-LMM, REGENIE and SNPtest. METAL met some problems: 1. METAL can generate two outputs, one is Effect(beta) + stdErr and other other is...