Difference between revisions of "Minimac3 Info File"
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==='''SNP'''=== | ==='''SNP'''=== | ||
| − | The SNP identifier for the variant. This is usually in the form of chr:position, but could be the rsid of the variant if the user had selected <code>--rsid</code> during the Minimac3 run. | + | The SNP identifier for the variant. This is usually in the form of '''chr:position''', but could be the rsid of the variant if the user had selected <code>--rsid</code> during the Minimac3 run. |
==='''REF''', '''ALT'''=== | ==='''REF''', '''ALT'''=== | ||
| Line 24: | Line 24: | ||
==='''DoseMAF'''=== | ==='''DoseMAF'''=== | ||
| − | This is the minor allele frequency of the variant in the imputed dosage data (and NOT the reference panel). [NOTE: The DoseMAF does NOT always correspond to the allele frequency of the | + | This is the minor allele frequency of the variant in the imputed dosage data (and NOT the reference panel). [NOTE: The '''DoseMAF''' does NOT always correspond to the allele frequency of the above '''Minor''' allele, since that is based on the reference panel minor allele frequency, and sometimes the imputed minor allele is different from the reference minor allele] |
| + | |||
| + | ==='''RefAF'''=== | ||
| + | |||
| + | This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the '''RefAF''' is the lesser than 0.5, then the '''ALT''' and '''Minor''' alleles are going to be same, if it is greater than 0.5, then they should be swapped. | ||
| + | |||
| + | |||
| + | |||
| + | ==='''AvgCall'''=== | ||
| + | |||
| + | This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped. | ||
| + | |||
| + | |||
| + | |||
| + | ==='''Rsq'''=== | ||
| + | |||
| + | This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped. | ||
| + | |||
| + | |||
| + | ==='''Genotyped'''=== | ||
| + | |||
| + | This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped. | ||
| + | |||
| + | |||
| + | ==='''LooRsq'''=== | ||
| + | |||
| + | This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped. | ||
| + | |||
| + | |||
| + | ==='''EmpR'''=== | ||
| + | |||
| + | This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped. | ||
| + | |||
| + | |||
| + | ==='''EmpRsq'''=== | ||
| + | |||
| + | This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped. | ||
| + | |||
| + | |||
| + | ==='''Dose1'''=== | ||
| + | |||
| + | This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped. | ||
| + | |||
| + | |||
| + | |||
| + | ==='''Dose2'''=== | ||
| + | |||
| + | This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped. | ||
= Download = | = Download = | ||
Revision as of 12:35, 18 September 2015
Introduction
Minimac3 is a lower memory and more computationally efficient implementation of minimac2. It is an algorithm for genotypic imputation that works on phased genotypes (say from MaCH) and is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.
This wiki page is designed to give users a detailed explanation of the info file outputted by Minimac3.
Info File Descriptors
The available options of Minimac3 are explained in detail below. See wiki page on Examples and Full list of Options for more details. There is also a wiki-page on Minimac3 Imputation Cookbook which is recommended for new users !
SNP
The SNP identifier for the variant. This is usually in the form of chr:position, but could be the rsid of the variant if the user had selected --rsid during the Minimac3 run.
REF, ALT
These are the reference and alternate alleles for the variant as imported from the reference panel file (either VCF or M3VCF)
Major, Minor
These are the major and minor alleles for the variant based on the reference allele frequency (and NOT imputed dosage frequency)
DoseMAF
This is the minor allele frequency of the variant in the imputed dosage data (and NOT the reference panel). [NOTE: The DoseMAF does NOT always correspond to the allele frequency of the above Minor allele, since that is based on the reference panel minor allele frequency, and sometimes the imputed minor allele is different from the reference minor allele]
RefAF
This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped.
AvgCall
This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped.
Rsq
This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped.
Genotyped
This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped.
LooRsq
This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped.
EmpR
This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped.
EmpRsq
This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped.
Dose1
This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped.
Dose2
This is the alternate allele frequency of the variant in the reference panel (NOT the minor allele frequency). If the RefAF is the lesser than 0.5, then the ALT and Minor alleles are going to be same, if it is greater than 0.5, then they should be swapped.
Download
Minimac3 is available as an undocumented release version. The source files (and binary executable) are available for download in Source Files and commonly used reference panels in VCF and M3VCF formats are available for download in Reference Panels.
Useful Wiki Pages
There are a few pages in this Wiki that may be useful to for Minimac3 users. Here are links to a few:
- Minimac3 Imputation Cookbook (Recommended for New Users!!)
Contact
In case of any queries and bugs please contact Sayantan Das.
