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"  

| <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).   

|-  

|-  

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

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

| 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>  

| 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]

| If ON, output files will be NOT bgzipped.

| 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.

|}

|}