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, 12:10, 21 January 2016
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| * External : [ftp://share.sph.umich.edu/vt resource bundle] | | * External : [ftp://share.sph.umich.edu/vt resource bundle] |
| * Internal : /net/fantasia/home/atks/ref/vt/grch37 | | * Internal : /net/fantasia/home/atks/ref/vt/grch37 |
| + | |
| + | GRCH37 set : Files are based on hs37d5.fa made by Heng Li. |
| + | |
| + | {| class="wikitable" |
| + | |- |
| + | ! scope="col"| data set |
| + | ! scope="col"| samples |
| + | ! scope="col"| snps/indels/complex/sv |
| + | ! scope="col"| description |
| + | |- |
| + | |1000G.v5 <br> |
| + | dbsnp138 <br> |
| + | 1000G.omni.chip <br> |
| + | mills <br> |
| + | mills.chip <br> |
| + | affy.exome.chip <br> |
| + | NA12878.broad.kb <br> |
| + | NA12878.v7.illumina.platinum <br> |
| + | mdust.bed.gz <br> |
| + | gencode.cds.bed.gz <br> |
| + | trf.bed.gz |
| + | | 0<br> |
| + | 0<br> |
| + | 2141<br> |
| + | 0<br> |
| + | 158<br> |
| + | 2122<br> |
| + | 1<br> |
| + | 1 <br> |
| + | NA <br> |
| + | NA <br> |
| + | NA |
| + | | 81316694/3296894/66806/59426 <br> |
| + | 10588965/2488793/69749/0 <br> |
| + | 2432554/5/0/0 <br> |
| + | 0/208753/0/0 <br> |
| + | 0/8904/0/0 <br> |
| + | 281875/34389/0/0 <br> |
| + | 281345/87389/152/0 <br> |
| + | 3702969/650764/13751/0 <br> |
| + | NA<br> |
| + | NA<br> |
| + | NA |
| + | |1000G v5. [1000G 2015?]<br> |
| + | derived from GATK's resource bundle that excludes 1000G variants.<br> |
| + | 1000G individuals typed on the omni chip [1000G 2015?]<br> |
| + | indels from [Mills 2006]<br> |
| + | indels from [Mills 2011]<br> |
| + | 1000G individuals and others typed on the affymetrix exome chip [1000G 2015?]<br> |
| + | from GATK's NA12878 knowledgebase.<br> |
| + | Illumina's platinum genomes version 7<br> |
| + | regions of low complexity annotated using mdust [Morgulis 2006]<br> |
| + | coding sequence regions based on GENCODE v19 annotations [Harrow 2012]<br> |
| + | 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 = |