General Information
- Yaw Nti-Addae
- Evan Rees
- Elizabeth Jones
Contents
Genotyping data management systems
System | Group | Contact | VM Hostname | phase |
|---|---|---|---|---|
JHI | @Sebastian Raubach | one | ||
Cornell GOBii | @Dave Matthews @Evan Rees | one | ||
CIRAD | @guilhem.sempere | one | ||
BTI | @Titima Tantikanjana | TWO | ||
MontyDB | Cornell McCouch Lab | @Francisco Agosto |
| TWO |
Broad Institute |
|
| TWO | |
Cornell Buckler Lab | Ask Ed |
| HOLD | |
Breeding Insight | @Moira Sheehan |
| HOLD | |
University of Washington | Dori? |
| HOLD | |
| Patrick |
| HOLD |
VM allocations
VM Hostname | Status | Server Pool | Assignment | username |
|---|---|---|---|---|
off | cbsugobii09 | Breedbase | breedbase | |
on | cbsugobii09 | GDM | gadm | |
on | cbsugobii10 | Gigwa | gigwa | |
off | cbsugobii10 | PHG | phg | |
|
|
|
|
|
on | cbsugobii11 | Germinate | jhi | |
| off | cbsugobii11 | MontyDB | montydb |
Each VM has the following resources:
8 CPUs
64 GB RAM
2 TB SSD
/storage mounted volume
/shared_data mounted volume
Datasets
Dataset | Format | Location |
|---|---|---|
Maize NAM | CSV | /shared_data/test_data/NAM_HM32/csv |
Simulated datasets |
|
|
polyploid data in VCF |
| Moira share a dataset - invite to next meeting |
indel data |
|
|
rice high density array | vcf | The Rice High Density Array is : 700K SNPs x ~1500 samples SNPs only vcf too Francisco loaded to Gigwa (own instance) already no problem http://rs-bt-mccouch4.biotech.cornell.edu/staged_data/CSHL_EVA_Release_HDRA.tar Hapmap: cbsugobiizvm19:/shared_data/test_data/genomics-systems-comparison/rice/Dataset.hmp.txt |
African rice |
| https://gigwa.ird.fr/gigwa/?module=AfricanRice available as vcf metadata availability?
|
3,000 rice genomes |
| too large? 29M SNPs |
lettuce Wageningen Public dataset | vcf | 12M markers x 500 accessions 3 vcfs - one SNPs, one indels, one structural variants 40 GBs https://www.nature.com/articles/s41588-021-00831-0/pub/CNSA/data2/CNP0000335/Other/variation |
Lettuce | hapmap flapjack | /shared_data/test_data/genomics-systems-comparison/lettuce/
chr1/
Lactuca__project1__2021-06-24__1152198variants__FLAPJACK.fjzip
Lactuca__project1__2021-06-24__1152198variants__HAPMAP.zip
markerlists.zip
full/
Lactuca__project1__2021-06-28__12983735variants__FLAPJACK.fjzip
Lactuca__project1__2021-06-28__12983735variants__HAPMAP.zip |
potato (polyploid) | VCF | /shared_data/test_data/genomics-systems-comparison/potato/
PRJNA414303.CHR5.filterNullGT.vcf.gz |