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, 21:00, 1 December 2016
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| '''Cloning from GitHub is recommened so that updates can be easily pulled back !!!''' | | '''Cloning from GitHub is recommened so that updates can be easily pulled back !!!''' |
| + | |
| + | = Reference Panels for Download = |
| + | |
| + | Some commonly used reference panels are available for download here: |
| + | |
| + | '''Chr X Haplotypes for 1000 Genomes Phase 3 have been updated on Oct 20 to include multi-allelic variants as well (split as bi-allelic variants) !!!''' |
| + | |
| + | {| class="wikitable" style="text-align:center" border="1" cellpadding="2" |
| + | |- bgcolor="lightgray" |
| + | ! width="150px" |Reference Panel |
| + | ! width="100px" |Number <br> of Samples |
| + | ! width="100px" |File Format |
| + | ! width="100px" |Parameter <br> Estimates <br> Available |
| + | ! width="120px" |Chromosomes |
| + | ! width="80px" |Link |
| + | |- |
| + | | rowspan=4 | '''1000 Genomes''' <br> |
| + | '''Phase 3''' <br> |
| + | (version 5) |
| + | | rowspan=4 style="text-align:center" | '''2,504''' |
| + | | '''VCF''' |
| + | | - |
| + | | 1-22,X |
| + | | [ftp://share.sph.umich.edu/minimac3/G1K_P3_VCF_Files.tar.gz Download] <!--[ftp://share.sph.umich.edu/minimac3/G1K_P3_VCF_Files.tar.gz Download]--> |
| + | |- |
| + | | rowspan=2 style="text-align:center" | '''M3VCF''' |
| + | | YES |
| + | | 1-22,X |
| + | | [ftp://share.sph.umich.edu/minimac3/G1K_P3_M3VCF_FILES_WITH_ESTIMATES.tar.gz Download] <!-- [ftp://share.sph.umich.edu/minimac3/G1K_P3_M3VCF_FILES_WITH_ESTIMATES.tar.gz Download]--> |
| + | |- |
| + | |NO |
| + | | 1-22,X |
| + | | [ftp://share.sph.umich.edu/minimac3/G1K_P3_M3VCF_FILES_NO_ESTIMATES.tar.gz Download] <!--[ftp://share.sph.umich.edu/minimac3/G1K_P3_M3VCF_FILES_NO_ESTIMATES.tar.gz Download]--> |
| + | |- |
| + | | '''VCF''','''M3VCF''' |
| + | | YES |
| + | | X |
| + | | [ftp://share.sph.umich.edu/minimac3/G1K_P3_CHR_X_VCF_M3VCF_FILES.tar.gz Download] <!--[ftp://share.sph.umich.edu/minimac3/G1K_P3_CHR_X_VCF_M3VCF_FILES.tar.gz Download]--> |
| + | |- |
| + | | rowspan=4 | '''1000 Genomes''' <br> |
| + | '''Phase 1''' <br> |
| + | (version 3) |
| + | | rowspan=4 | '''1,092''' |
| + | | '''VCF''' |
| + | | - |
| + | | 1-22,X |
| + | | [ftp://share.sph.umich.edu/minimac3/G1K_P1_VCF_Files.tar.gz Download] |
| + | |- |
| + | | rowspan=2 style="text-align:center" | '''M3VCF''' |
| + | | YES |
| + | | 1-22,X |
| + | | [ftp://share.sph.umich.edu/minimac3/G1K_P1_M3VCF_FILES_WITH_ESTIMATES.tar.gz Download] |
| + | |- |
| + | | NO |
| + | | 1-22,X |
| + | | [ftp://share.sph.umich.edu/minimac3/G1K_P1_M3VCF_FILES_NO_ESTIMATES.tar.gz Download] |
| + | |- |
| + | | '''VCF''','''M3VCF''' |
| + | | YES |
| + | | X |
| + | | [ftp://share.sph.umich.edu/minimac3/G1K_P1_CHR_X_VCF_M3VCF_FILES.tar.gz Download] <!--[ftp://share.sph.umich.edu/minimac3/G1K_P1_CHR_X_VCF_M3VCF_FILES.tar.gz Download]--> |
| + | |} |