Line 1,729: |
Line 1,729: |
| | | |
| = 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 |
− |
| |
− | GRCH37 set : Files are based on hs37d5.fa made by Heng Li.
| |
| | | |
| {| class="wikitable" | | {| class="wikitable" |
Line 1,750: |
Line 1,752: |
| NA12878.broad.kb <br> | | NA12878.broad.kb <br> |
| NA12878.v7.illumina.platinum <br> | | NA12878.v7.illumina.platinum <br> |
− | mdust.bed.gz <br>
| |
− | gencode.v19.cds.bed.gz <br>
| |
− | trf.bed.gz
| |
| | 0<br> | | | 0<br> |
| 0<br> | | 0<br> |
Line 1,761: |
Line 1,760: |
| 1<br> | | 1<br> |
| 1 <br> | | 1 <br> |
− | NA <br>
| |
− | NA <br>
| |
− | NA
| |
| | 81316694/3296894/66806/59426 <br> | | | 81316694/3296894/66806/59426 <br> |
| 10588965/2488793/69749/0 <br> | | 10588965/2488793/69749/0 <br> |
Line 1,772: |
Line 1,768: |
| 281345/87389/152/0 <br> | | 281345/87389/152/0 <br> |
| 3702969/650764/13751/0 <br> | | 3702969/650764/13751/0 <br> |
− | NA<br>
| |
− | NA<br>
| |
− | NA
| |
| |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> |
Line 1,783: |
Line 1,776: |
| 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 |
− |
| |
− | GRCH38 set : Files are based on [https://github.com/lh3/bwa/blob/master/README-alt.md hs38DH.fa] made by Heng Li.
| |
| | | |
| {| class="wikitable" | | {| class="wikitable" |
Line 1,806: |
Line 1,822: |
| 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 |
− | mdust.bed.gz <br>
| |
− | gencode.v27.cds.bed.gz <br>
| |
− | trf.bed.gz
| |
| | 0<br> | | | 0<br> |
| 0<br> | | 0<br> |
Line 1,817: |
Line 1,830: |
| 2122<br> | | 2122<br> |
| 1<br> | | 1<br> |
− | 1 <br> | + | 1 |
− | NA <br>
| |
− | NA <br>
| |
− | NA
| |
| | 81316694/3296894/66806/59426 <br> | | | 81316694/3296894/66806/59426 <br> |
| 10588965/2488793/69749/0 <br> | | 10588965/2488793/69749/0 <br> |
Line 1,828: |
Line 1,838: |
| 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 |
− | NA<br>
| |
− | NA<br>
| |
− | NA
| |
| |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> |
Line 1,839: |
Line 1,846: |
| 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 |
− | regions of low complexity annotated using mdust [Morgulis 2006]<br>
| |
− | coding sequence regions based on GENCODE v27 annotations [Harrow 2012]<br>
| |
− | tandem repeat finder STRs from lobSTR's resource bundle [Gymrek 2012]
| |
| |} | | |} |
| | | |