Difference between revisions of "M3vcftools Usage"
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| <font face=Courier>--check</font> | | <font face=Courier>--check</font> | ||
| This option does some extra verification while reading M3VCF files. If your program crashed for some reason, try re-running it with this option ON and see if it gives an error message. | | This option does some extra verification while reading M3VCF files. If your program crashed for some reason, try re-running it with this option ON and see if it gives an error message. | ||
| + | |} | ||
| + | |||
| + | ===OUTPUT FILE OPTIONS=== | ||
| + | |||
| + | {| border="1" cellpadding="2" | ||
| + | |- bgcolor="lightgray" | ||
| + | ! scope="col" width="350px" | Parameter | ||
| + | ! scope="col" width="1225px" | Description | ||
| + | |- | ||
| + | | <font face=Courier>--'''out''' <output_prefix></font> | ||
| + | | This option defines the output prefix for all files that are generated by m3vcftools. Default Value: <font face=Courier>Vm3vcftools.Output</font face=Courier>. | ||
| + | |- | ||
| + | | <font face=Courier>--'''recode'''</font> | ||
| + | | This option is used for converting input VCF files to output M3VCF files. It is also used when you import a M3VCF file on a subset of variants or subset of samples and would wish to re-compress the sub-set file for efficient analysis in the future. | ||
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Revision as of 21:39, 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 |
|---|---|
| --vcf or --in <input_filename> | This option defines the VCF file or M3VCF file (DOES NOT support missing or multi-allelic variants now, will update soon). |
| --check | This option does some extra verification while reading M3VCF files. If your program crashed for some reason, try re-running it with this option ON and see if it gives an error message. |
OUTPUT FILE OPTIONS
| Parameter | Description |
|---|---|
| --out <output_prefix> | This option defines the output prefix for all files that are generated by m3vcftools. Default Value: Vm3vcftools.Output. |
| --recode | This option is used for converting input VCF files to output M3VCF files. It is also used when you import a M3VCF file on a subset of variants or subset of samples and would wish to re-compress the sub-set file for efficient analysis in the future. |
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.
