Changes

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==

 

 

===INPUT FILE OPTIONS===

{| border="1" cellpadding="2"  

{| border="1" cellpadding="2"  

|- bgcolor="lightgray"

|- bgcolor="lightgray"

!  scope="col" width="200px" | Parameter  

!  scope="col" width="350px" | Parameter  

!  scope="col" width="1225px" | Description

!  scope="col" width="1225px" | Description

|-  

|-  

| <font face=Courier>--refHaps filename </font>  

| <font face=Courier>--'''vcf''' or --'''in''' <input_filename></font>

|  VCF file or <font face=Courier>M3VCF</font> file containing haplotype data for reference panel.

|  This option defines the <font face=Courier>VCF</font face=Courier> file or <font face=Courier>M3VCF</font> file (DOES NOT support missing or multi-allelic variants now, will update soon).

|-  

|-  

| <font face=Courier>--passOnly</font>  

| <font face=Courier>--'''check'''</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).  

| 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. 

 

 

 

 

!  scope="col" width="350px" | Parameter

! scope="col" width="1225px" | Description

|-  

|-  

| <font face=Courier>--haps filename </font>

| <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>m3vcftools.Output</font face=Courier>.

| <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>--'''recode'''</font>  

| Prefix for all output files generated. By default: <font face=Courier>[Minimac3.Output]</font>

| This option is used for converting input <font face=Courier>VCF</font> files to output <font face=Courier>M3VCF</font> files. It is also used when you import a <font face=Courier>M3VCF</font> 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.  

|}

| <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>

==SITE FILTERING OPTIONS==

| If ON, output files will be NOT bgzipped.  

 

|-

 

===POSITION FILTERING===

 

{| border="1" cellpadding="2"

| <font face=Courier>--hapOutput</font>

|- bgcolor="lightgray"

!  scope="col" width="350px" | Parameter

!  scope="col" width="1225px" | Description

| <font face=Courier>--format</font>

| Specifies which fields to output for the FORMAT field in output VCF file. Available handles: <font face=Courier>GT,DS,GP </font>[Default: <font face=Courier>GT,DS</font>]

|-

| <font face=Courier>--allTypedSites</font>

| Also Includes variants that were genotyped but NOT in the reference panel in the output files (and imputes any missing data in such variants to the major allele frequency).

| <font face=Courier>--chr 22</font>

| Chromosome number for which we will carry out imputation.

|-  

|-  

| <font face=Courier>--start 100000</font>

| <font face=Courier>--'''chr''' <chromosome></font>

| Start position for imputation by chunking. Would not work without <font face=Courier>--chr</font> option.

| This option includes all sites with identifiers matching the value of <font face=Courier><chromosome></font face=Courier>. (m3vcftools only handles single chromosome files)

|-  

|-  

| <font face=Courier>--end 200000</font>

| <font face=Courier>--'''from-bp''' <integer></font>   <br>  <font face=Courier>--'''to-bp''' <integer></font>

| End position for imputation by chunking. Would not work without <font face=Courier>--chr</font> option.

| This option specifies a '''lower / upper bound (inclusive)''' for the range of sites to be processed. This option must be used in conjunction with <font face=Courier>--'''chr''' </font>.

  | <font face=Courier>--window 5000</font>

| Length of buffer region on either side of <font face=Courier>--start</font> and <font face=Courier>--end</font>. By default = 0.

|-  

|-  

| <font face=Courier>--rec</font>

| <font face=Courier>--'''positions''' <filename></font>  <br> <font face=Courier>--'''exclude-positions''' <filename></font>  

| Recombination File from previous run of Minimac/Minimac3. (<font face=Courier>--err</font> parameter must also be provided, if using this handle)

| This option is used to '''include / exclude''' a set of sites on the basis of list of positions in the given file. Each line of the input file should contain a (tab-separated) chromosome and position. The file can have comment lines that start with a "#", they will be ignored. Thus, <font face=Courier>M3VCF</font face=Courier> or <font face=Courier>VCF</font face=Courier> files can be used as <font face=Courier><filename></font face=Courier>.

 

 

 

 

 

 

|-  

|-  

| <font face=Courier>--err</font>

| <font face=Courier>--'''freq '''</font>

| Error File from previous run of Minimac/Minimac3. (<font face=Courier>--rec</font> parameter must also be provided, if using this handle)

| This option outputs the allele frequency for each site in a file with suffix <font face=Courier>".frq"</font face=Courier>.

|-  

|-  

| <font face=Courier>--rounds 5</font>

| <font face=Courier>--'''counts '''</font>

| Rounds of optimization for model parameters, which describe population recombination rates and per SNP error rates. By default = 5.

| This option outputs the raw allele count for each site in a file with suffix <font face=Courier>".frq.count"</font face=Courier>.

|}

| <font face=Courier>--states 200</font>

 

| Maximum number of reference (or target) haplotypes to be examined during parameter optimization. By default = 200.

 

 

===OUTPUT LINKAGE (LD) STATISTICS===

 

!  scope="col" width="1225px" | Description

|-  

|-  

| <font face=Courier>--help</font>

| <font face=Courier>--'''hap-r2'''</font>

| A short help on options.

| This option outputs summary of linkage disequilibrium (reported as r2, D and D' statistics using phased haplotypes) in a file with suffix <font face=Courier>".hap.ld"</font face=Courier>. These statistics are only calculated for phased, bi-allelic sites.

|-  

|-  

| <font face=Courier>--cpus 5</font>

| <font face=Courier>--'''ld-window''' <integer>  </br> --'''ld-window-min''' <integer></font>

| Number of cpus for parallel computing. Would work only with Minimac3-omp.

| This optional parameter defines the '''maximum / minimum''' number of variants between the variants being analyzed.

|-  

|-  

| <font face=Courier>--noPhoneHome</font>

| <font face=Courier>--'''ld-window-bp''' <integer>  </br> --'''ld-window-bp-min''' <integer></font>

| If ON, code will NOT send a SUCCESS/FAILURE status of the execution to home server.

| This optional parameter defines the '''maximum / minimum''' number of physical bases between the variants being analyzed.

|-  

|-  

| <font face=Courier>--phoneHomeThinning 50</font>

| <font face=Courier>--'''min-r2''' <float></font>

| Percentage probability of sending SUCCESS/FAILURE status of the execution to home server [Default: 50%]

| This optional parameter sets a minimum value of r2, below with LD statistics are NOT reported. It can be used in conjunction with the above parameters.

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