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| 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).
| 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).
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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.
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===OUTPUT FILE OPTIONS===
===OUTPUT FILE OPTIONS===
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==INPUT FILE OPTIONS==
==SITE FILTERING OPTIONS==
===POSITION FILTERING===
{| border="1" cellpadding="2"
|- bgcolor="lightgray"
! scope="col" width="350px" | Parameter
! scope="col" width="1225px" | Description
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| <font face=Courier>--'''chr''' <chromosome></font>
| This option includes all sites with identifiers matching the value of <font face=Courier><chromosome></font face=Courier>. (m3vcftools only handles single chromosome files)
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| <font face=Courier>--'''from-bp''' <integer></font> <br> <font face=Courier>--'''to-bp''' <integer></font>
| 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>.
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| <font face=Courier>--'''positions''' <filename></font> <br> <font face=Courier>--'''exclude-positions''' <filename></font>
| 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>.
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==OUTPUT OPTIONS==
===OUTPUT ALLELE STATISTICS===
{| border="1" cellpadding="2"
{| border="1" cellpadding="2"
|- bgcolor="lightgray"
|- bgcolor="lightgray"
! scope="col" width="250px" | Parameter
! scope="col" width="350px" | Parameter
! scope="col" width="1225px" | Description
! scope="col" width="1225px" | Description
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| <font face=Courier>--refHaps filename </font>
| <font face=Courier>--'''freq '''</font>
| VCF file or <font face=Courier>M3VCF</font> file containing haplotype data for reference panel.
| This option outputs the allele frequency for each site in a file with suffix <font face=Courier>".frq"</font face=Courier>.
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| <font face=Courier>--'''counts '''</font>
| This option outputs the raw allele count for each site in a file with suffix <font face=Courier>".frq.count"</font face=Courier>.
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===OUTPUT LINKAGE (LD) STATISTICS===
{| border="1" cellpadding="2"
|- bgcolor="lightgray"
! scope="col" width="350px" | Parameter
! scope="col" width="1225px" | Description
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| <font face=Courier>--'''hap-r2'''</font>
| 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.
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| <font face=Courier>--'''ld-window''' <integer> </br> --'''ld-window-min''' <integer></font>
| This optional parameter defines the '''maximum / minimum''' number of variants between the variants being analyzed.
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| <font face=Courier>--'''ld-window-bp''' <integer> </br> --'''ld-window-bp-min''' <integer></font>
| This optional parameter defines the '''maximum / minimum''' number of physical bases between the variants being analyzed.
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| <font face=Courier>--passOnly</font>
| <font face=Courier>--'''min-r2''' <float></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 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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