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Minimac4

2,216 bytes added, 21:00, 1 December 2016
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'''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]-->
|}
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