Difference between revisions of "Emerald"
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | + | Tools for rapid on-the-fly LD calculation. | |
| − | Tools for rapid on-the-fly LD calculation | + | |
| − | + | Exploits sparsity and haplotype structure to efficiently calculate LD | |
| − | + | ||
| − | + | Uses tabix indexes to support rapid querying of genomic regions | |
| − | + | ||
| + | Supports VCF (phased or unphased) and M3VCF formats | ||
| + | |||
| + | Supports integration with Python and R | ||
<!--Modules--> | <!--Modules--> | ||
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{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
sh example.sh | sh example.sh | ||
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example command: bin/emeraLD -i example/chr20.1KG.25K_m.m3vcf.gz --region 20:60479-238197 --out example | example command: bin/emeraLD -i example/chr20.1KG.25K_m.m3vcf.gz --region 20:60479-238197 --out example | ||
| + | |||
emeraLD v0.1 (c) 2018 corbin quick (corbinq@gmail.com) | emeraLD v0.1 (c) 2018 corbin quick (corbinq@gmail.com) | ||
| + | |||
reading from m3vcf file... | reading from m3vcf file... | ||
| + | |||
processed genotype data for 5008 haplotypes... | processed genotype data for 5008 haplotypes... | ||
| + | |||
calculating LD for 1989 SNPs... | calculating LD for 1989 SNPs... | ||
| + | |||
done!! thanks for using emeraLD | done!! thanks for using emeraLD | ||
Latest revision as of 19:16, 29 October 2023
Description
Tools for rapid on-the-fly LD calculation.
Exploits sparsity and haplotype structure to efficiently calculate LD
Uses tabix indexes to support rapid querying of genomic regions
Supports VCF (phased or unphased) and M3VCF formats
Supports integration with Python and R
Environment Modules
Run module spider emerald to find out what environment modules are available for this application.
System Variables
- HPC_EMERALD_DIR - installation directory
- HPC_EMERALD_BIN - executable directory
Performance
sh example.sh
example command: bin/emeraLD -i example/chr20.1KG.25K_m.m3vcf.gz --region 20:60479-238197 --out example
emeraLD v0.1 (c) 2018 corbin quick (corbinq@gmail.com)
reading from m3vcf file...
processed genotype data for 5008 haplotypes...
calculating LD for 1989 SNPs...
done!! thanks for using emeraLD
real 0m1.145s user 0m1.036s sys 0m0.023s
Citation
If you publish research that uses emerald you can cite Quick et al. (2018) Bioinformatics.