1,102
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Resource Bundle
= Resource Bundle =
= Resource Bundle =
== GRCh37 ==
Files are based on hs37d5.fa made by Heng Li.
* 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
{| class="wikitable"
{| class="wikitable"
NA12878.broad.kb <br>
NA12878.broad.kb <br>
NA12878.v7.illumina.platinum <br>
NA12878.v7.illumina.platinum <br>
| 0<br>
| 0<br>
0<br>
0<br>
1<br>
1<br>
1 <br>
1 <br>
| 81316694/3296894/66806/59426 <br>
| 81316694/3296894/66806/59426 <br>
10588965/2488793/69749/0 <br>
10588965/2488793/69749/0 <br>
281345/87389/152/0 <br>
281345/87389/152/0 <br>
3702969/650764/13751/0 <br>
3702969/650764/13751/0 <br>
|1000G v5. [1000G 2015]<br>
|1000G v5. [1000G 2015]<br>
derived from GATK's resource bundle that excludes 1000G variants.<br>
derived from GATK's resource bundle that excludes 1000G variants.<br>
from GATK's NA12878 knowledgebase.<br>
from GATK's NA12878 knowledgebase.<br>
Illumina's platinum genomes version 7<br>
Illumina's platinum genomes version 7<br>
regions of low complexity annotated using mdust [Morgulis 2006]<br>
|}
{| class="wikitable"
|-
! scope="col"| data set
! scope="col"| no. of regions
! scope="col"| total bases
! scope="col"| description
|-
|mdust.bed.gz <br>
gencode.v19.cds.bed.gz <br>
trf.bed.gz
| NA <br>
NA <br>
NA
| NA<br>
NA<br>
NA
|regions of low complexity annotated using mdust [Morgulis 2006]<br>
coding sequence regions based on GENCODE v19 annotations [Harrow 2012]<br>
coding sequence regions based on GENCODE v19 annotations [Harrow 2012]<br>
tandem repeat finder STRs from lobSTR's resource bundle [Gymrek 2012]
tandem repeat finder STRs from lobSTR's resource bundle [Gymrek 2012]
|}
|}
== GRCh38 ==
Files are based on [https://github.com/lh3/bwa/blob/master/README-alt.md hs38DH.fa] made by Heng Li.
* External : [ftp://share.sph.umich.edu/vt resource bundle]
* Internal : /net/fantasia/home/atks/ref/vt/grch38
* Internal : /net/fantasia/home/atks/ref/vt/grch38
{| class="wikitable"
{| class="wikitable"
affy.exome.chip <br>
affy.exome.chip <br>
NA12878.broad.kb <br>
NA12878.broad.kb <br>
NA12878.v7.illumina.platinum <br>
NA12878.v7.illumina.platinum
| 0<br>
| 0<br>
0<br>
0<br>
2122<br>
2122<br>
1<br>
1<br>
1 <br>
1
| 81316694/3296894/66806/59426 <br>
| 81316694/3296894/66806/59426 <br>
10588965/2488793/69749/0 <br>
10588965/2488793/69749/0 <br>
281875/34389/0/0 <br>
281875/34389/0/0 <br>
281345/87389/152/0 <br>
281345/87389/152/0 <br>
3702969/650764/13751/0 <br>
3702969/650764/13751/0
|1000G v5. [1000G 2015]<br>
|1000G v5. [1000G 2015]<br>
derived from GATK's resource bundle that excludes 1000G variants.<br>
derived from GATK's resource bundle that excludes 1000G variants.<br>
1000G individuals and others typed on the affymetrix exome chip [1000G 2015]<br>
1000G individuals and others typed on the affymetrix exome chip [1000G 2015]<br>
from GATK's NA12878 knowledgebase.<br>
from GATK's NA12878 knowledgebase.<br>
Illumina's platinum genomes version 7<br>
Illumina's platinum genomes version 7
|}
|}
