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, 22:57, 3 November 2017
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| | * Internal : /net/fantasia/home/atks/ref/vt/grch37 | | * Internal : /net/fantasia/home/atks/ref/vt/grch37 |
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| − | Read here for [ftp://share.sph.umich.edu/vt/grch38/readme.txt contents]. | + | Read here for [ftp://share.sph.umich.edu/vt/grch37/readme.txt contents]. |
| | | | |
| | == GRCh38 == | | == GRCh38 == |
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| | * Internal : /net/fantasia/home/atks/ref/vt/grch38 | | * Internal : /net/fantasia/home/atks/ref/vt/grch38 |
| | | | |
| − | {| class="wikitable"
| + | Read here for [ftp://share.sph.umich.edu/vt/grch38/readme.txt contents]. |
| − | |-
| |
| − | ! scope="col"| data set
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| − | ! scope="col"| samples
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| − | ! scope="col"| snps/indels/complex/sv
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| − | ! scope="col"| description
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| − | |-
| |
| − | |1000G.v5 <br>
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| − | dbsnp138 <br>
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| − | 1000G.omni.chip <br>
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| − | mills <br>
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| − | mills.chip <br>
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| − | affy.exome.chip <br>
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| − | NA12878.broad.kb <br>
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| − | NA12878.v7.illumina.platinum
| |
| − | | 0<br>
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| − | 0<br>
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| − | 2141<br>
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| − | 0<br>
| |
| − | 158<br>
| |
| − | 2122<br>
| |
| − | 1<br>
| |
| − | 1
| |
| − | | 81316694/3296894/66806/59426 <br>
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| − | 10588965/2488793/69749/0 <br>
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| − | 2432554/5/0/0 <br>
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| − | 0/208753/0/0 <br>
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| − | 0/8904/0/0 <br>
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| − | 281875/34389/0/0 <br>
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| − | 281345/87389/152/0 <br>
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| − | 3702969/650764/13751/0
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| − | |1000G v5. [1000G 2015]<br>
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| − | derived from GATK's resource bundle that excludes 1000G variants.<br>
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| − | 1000G individuals typed on the omni chip [1000G 2015]<br>
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| − | indels from [Mills 2006]<br>
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| − | indels from [Mills 2011]<br>
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| − | 1000G individuals and others typed on the affymetrix exome chip [1000G 2015]<br>
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| − | from GATK's NA12878 knowledgebase.<br>
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| − | Illumina's platinum genomes version 7
| |
| − | |}
| |
| − | | |
| − | | |
| − | {| class="wikitable"
| |
| − | |-
| |
| − | ! scope="col"| data set
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| − | ! scope="col"| no. of regions
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| − | ! scope="col"| total bases
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| − | ! scope="col"| description
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| − | |-
| |
| − | |mdust.bed.gz <br>
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| − | gencode.v27.cds.bed.gz <br>
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| − | trf.lobstr.bed.gz
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| − | | NA <br>
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| − | NA <br>
| |
| − | NA
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| − | | NA<br>
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| − | NA<br>
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| − | NA
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| − | |regions of low complexity annotated using mdust [Morgulis 2006]<br>
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| − | coding sequence regions based on GENCODE v27 annotations [Harrow 2012]<br>
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| − | tandem repeat finder STRs from lobSTR's resource bundle [Gymrek 2012]
| |
| − | |}
| |
| − | | |
| − | Note: Please let me know if I did not cite a resource properly.
| |
| | | | |
| | = FAQ = | | = FAQ = |
