Mercurial > repos > pcingola > snpeff
comparison snpEff/snpEff.config @ 0:481a95ca5339
Migrated tool version 0.9 from old tool shed archive to new tool shed repository
| author | pcingola |
|---|---|
| date | Tue, 07 Jun 2011 17:08:59 -0400 |
| parents | |
| children | 2cf01e805427 |
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| -1:000000000000 | 0:481a95ca5339 |
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| 1 | |
| 2 # Interval data is stored here | |
| 3 data_dir = /usr/local/snpEff/data/ | |
| 4 | |
| 5 # Store cache files here | |
| 6 cache_dir = /tmp | |
| 7 | |
| 8 # Comma separated list of genomes | |
| 9 genomes : hg37, mm37 | |
| 10 | |
| 11 # For each genome 'XX' a set of attributes are defined: | |
| 12 # - XX.genome : The name of this genome | |
| 13 # - XX.chromosomes : A comma separated list of chromosome names | |
| 14 # - XX.fasta_dir : The directory where fasta files of this genome are located | |
| 15 # - XX.chromo_fasta_files : A comma separated list of the fasta files (one per chromosome). | |
| 16 # WARNING: They must be in the same order as the XX.chromosomes list | |
| 17 # | |
| 18 # Note: Attributes XX.fasta_dir and XX.chromo_fasta_files are only needed if you are building the data | |
| 19 # structures yourself. If you are using a pre-built file, you can leave both of them unassigned. | |
| 20 | |
| 21 | |
| 22 # Human genome, version hg37 | |
| 23 hg37.genome : Human | |
| 24 hg37.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y | |
| 25 hg37.fasta_dir : /data/genomes/hg37/ | |
| 26 hg37.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chr20.fa, chr21.fa, chr22.fa, chrX.fa, chrY.fa | |
| 27 | |
| 28 # Mouse genome, version mm37 | |
| 29 mm37.genome : Mouse | |
| 30 mm37.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, X, Y | |
| 31 mm37.fasta_dir : /data/genomes/mm37/ | |
| 32 mm37.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chrX.fa, chrY.fa |