Difference between revisions of "M3vcftools Usage"

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The following table gives a brief description of all the parameters of '''m3vcftools '''. The software is in a very developmental mode and new options are going to be added regularly. '''Please join our NEW [https://groups.google.com/forum/embed/?place=forum/m3vcftools-help&umich.edu mailing list] to get updates about future options that are added or new option requests that you might want early'''. User could also email their queries/feedback to  [mailto:sayantan@umich.edu Sayantan Das].
 
The following table gives a brief description of all the parameters of '''m3vcftools '''. The software is in a very developmental mode and new options are going to be added regularly. '''Please join our NEW [https://groups.google.com/forum/embed/?place=forum/m3vcftools-help&umich.edu mailing list] to get updates about future options that are added or new option requests that you might want early'''. User could also email their queries/feedback to  [mailto:sayantan@umich.edu Sayantan Das].
  
−
==INPUT FILE OPTIONS==
+
==BASIC OPTIONS==
 +
 
 +
 
 +
===INPUT FILE OPTIONS===
  
 
{| border="1" cellpadding="2"  
 
{| border="1" cellpadding="2"  
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| <font face=Courier>--passOnly</font>  
 
| <font face=Courier>--passOnly</font>  
 
| If ON, only variants will FILTER=PASS will be recorded from reference VCF file (does NOT work on <font face=Courier>M3VCF</font> files yet).   
 
| If ON, only variants will FILTER=PASS will be recorded from reference VCF file (does NOT work on <font face=Courier>M3VCF</font> files yet).   
 +
|}
 +
 +
==INPUT FILE OPTIONS==
 +
 +
{| border="1" cellpadding="2"
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|- bgcolor="lightgray"
 +
!  scope="col" width="200px" | Parameter
 +
!  scope="col" width="1225px" | Description
 
|-  
 
|-  
−
| <font face=Courier>--haps filename </font>
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| <font face=Courier>--refHaps filename </font>  
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| File containing haplotype data for target (gwas) samples. Must be a VCF file.
+
| VCF file or <font face=Courier>M3VCF</font> file containing haplotype data for reference panel.
−
|-
 
−
| <font face=Courier>--processReference</font>  
 
−
| This option will only convert an input VCF file to M3VCF format (maybe for a later run of imputation). If this option is ON, no imputation would be performed and thus all other parameters will be ignored (of course, except for parameters on Reference Haplotypes and Subsetting Options). This option also does parameter estimation using the reference panel and saves them in the M3VCF file (the estimation can be skipped with <font face=Courier>rounds = 0</font>)
 
 
|-  
 
|-  
−
| <font face=Courier>--prefix output </font>
+
| <font face=Courier>--passOnly</font>  
−
| Prefix for all output files generated. By default: <font face=Courier>[Minimac3.Output]</font>
+
| If ON, only variants will FILTER=PASS will be recorded from reference VCF file (does NOT work on <font face=Courier>M3VCF</font> files yet).
−
|- 
 
−
| <font face=Courier>--updateModel</font>
 
−
| If ON, saved parameter estimates read from a M3VCF file will be further updated using the gwas samples. Will be ignored if VCF reference file. [Default: OFF]
 
−
|-
 
−
| <font face=Courier>--nobgzip</font>
 
−
| If ON, output files will be NOT bgzipped.
 
−
|-
 
−
| <font face=Courier>--doseOutput</font>
 
−
| If ON, imputed data will be output as dosage file as well [Default: OFF].
 
−
|-
 
−
| <font face=Courier>--cpus 5</font>
 
−
| Number of cpus for parallel computing. Would work only with Minimac3-omp.
 
−
|-
 
−
| <font face=Courier>--noPhoneHome</font>
 
−
| If ON, code will NOT send a SUCCESS/FAILURE status of the execution to home server.
 
−
|-
 
−
| <font face=Courier>--phoneHomeThinning 50</font>
 
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| Percentage probability of sending SUCCESS/FAILURE status of the execution to home server [Default: 50%]
 
 
|}
 
|}
  

Revision as of 21:29, 18 October 2015

Introduction

m3vcftools is a tool (exactly similar to vcftools) but will be much faster and can be used for simple data query and basic summary like allele frequency, linkage-r2 calculation, etc. m3vcftools is ideal for mega reference panels like Haplotye Reference Consortium (HRC) with over 32,000 samples where m3vcftools is 70-90 times faster than vcftools (18 mins vs 28 hours) in calculating AF or LD summaries.

This wiki page gives users a full list of all the available options on m3vcftools .

Full List of Options

The following table gives a brief description of all the parameters of m3vcftools . The software is in a very developmental mode and new options are going to be added regularly. Please join our NEW mailing list to get updates about future options that are added or new option requests that you might want early. User could also email their queries/feedback to Sayantan Das.

BASIC OPTIONS

INPUT FILE OPTIONS

Parameter Description
--refHaps filename VCF file or M3VCF file containing haplotype data for reference panel.
--passOnly If ON, only variants will FILTER=PASS will be recorded from reference VCF file (does NOT work on M3VCF files yet).

INPUT FILE OPTIONS

Parameter Description
--refHaps filename VCF file or M3VCF file containing haplotype data for reference panel.
--passOnly If ON, only variants will FILTER=PASS will be recorded from reference VCF file (does NOT work on M3VCF files yet).

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:

Contact

In case of any queries and bugs please contact Sayantan Das.

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