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1,367 bytes removed ,  21:57, 3 November 2017
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* Internal : /net/fantasia/home/atks/ref/vt/grch37
 
* Internal : /net/fantasia/home/atks/ref/vt/grch37
   −
Read here for [ftp://share.sph.umich.edu/vt/grch38/readme.txt contents].
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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
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{| class="wikitable"
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Read here for [ftp://share.sph.umich.edu/vt/grch38/readme.txt contents].
|-
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! 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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|-
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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
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| 0<br>
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0<br>
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2141<br>
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0<br>
  −
158<br>
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2122<br>
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1<br>
  −
1
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| 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
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|}
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  −
 
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{| class="wikitable"
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|-
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! 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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|-
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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>
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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]
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|}
  −
 
  −
Note:  Please let me know if I did not cite a resource properly.
      
= FAQ =
 
= FAQ =
1,102

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