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infrastructure:solu [11.10.2019 19:12] Teemu Kuulasmaa |
infrastructure:solu [14.03.2020 13:58] Teemu Kuulasmaa [Available reference data set] |
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- | ## Available reference data set | + | ### Available reference data set |
All the available reference data sets are provided as-is. They are unmodified copies of the original files. | All the available reference data sets are provided as-is. They are unmodified copies of the original files. | ||
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URL: [[https:// | URL: [[https:// | ||
- | Following variants can be found from the ** /apps/genomes/gnomAD ** folder. | + | Following variants can be found from the ** /research/groups/ |
^Data set ^Version^ | ^Data set ^Version^ | ||
|Exome variants (.vcf.bgz, tbi) | | |Exome variants (.vcf.bgz, tbi) | | ||
- | |Exome calling regions (.interval_list) | | + | |Exome calling regions (.interval list) | |
|Genome variants (.vcf.bgz, tbi) | |Genome variants (.vcf.bgz, tbi) | ||
- | |Genome calling regions (.interval_list) | | + | |Genome calling regions (.interval list) | |
|Structural variants (.vcf.gz, tbi) | | |Structural variants (.vcf.gz, tbi) | | ||
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In the terminal, you can see the list of available software packages by command | In the terminal, you can see the list of available software packages by command | ||
- | 'modul avail' | + | 'modul avail' |
- | homer/ | + | |
- | bamtools/ | + | |
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- | | + | blast-plus/2.7.1 |
- | bowtie/1.2 fastx-toolkit/ | + | |
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### Lmod Module Environment | ### Lmod Module Environment |