M3vcftools Usage - Revision history

Santy.8128: /* Full List of Options */

2015-10-19T02:04:03Z

Full List of Options

← Older revision		Revision as of 22:04, 18 October 2015
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	\| 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===		===OUTPUT FILE OPTIONS===
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	==SITE FILTERING OPTIONS==		==SITE FILTERING OPTIONS==


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

Santy.8128: /* SITE FILTERING OPTIONS */

2015-10-19T02:03:37Z

SITE FILTERING OPTIONS

← Older revision		Revision as of 22:03, 18 October 2015
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	\| 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>.		\| 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>.

			\|}


			==OUTPUT OPTIONS==


			===OUTPUT ALLELE STATISTICS===

			{\| border="1" cellpadding="2"
			\|- bgcolor="lightgray"
			! scope="col" width="350px" \| Parameter
			! scope="col" width="1225px" \| Description
			\|-
			\| <font face=Courier>--'''freq '''</font>
			\| This option outputs the allele frequency for each site in a file with suffix <font face=Courier>".frq"</font face=Courier>.
			\|-
			\| <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>.
			\|}


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

			{\| border="1" cellpadding="2"
			\|- bgcolor="lightgray"
			! scope="col" width="350px" \| Parameter
			! scope="col" width="1225px" \| Description
			\|-
			\| <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.
			\|-
			\| <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.
			\|-
			\| <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.
			\|-
			\| <font face=Courier>--'''min-r2''' <float></font>
			\| 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.
	\|}		\|}

Santy.8128: /* SITE FILTERING OPTIONS */

2015-10-19T01:54:20Z

SITE FILTERING OPTIONS

← Older revision		Revision as of 21:54, 18 October 2015
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	\| 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.		\| 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.
	\|}		\|}



	==SITE FILTERING OPTIONS==		==SITE FILTERING OPTIONS==


	===POSITION FILTERING===		===POSITION FILTERING===

Santy.8128: /* POSITION FILTERING */

2015-10-19T01:54:07Z

POSITION FILTERING

← Older revision		Revision as of 21:54, 18 October 2015
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	\|-		\|-
	\| <font face=Courier>--'''positions''' <filename></font> <br> <font face=Courier>--'''exclude-positions''' <filename></font>		\| <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, M3VCF or VCF files can be used as <filename>		\| 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>.

	\|}		\|}

Santy.8128: /* POSITION FILTERING */

2015-10-19T01:52:51Z

POSITION FILTERING

← Older revision		Revision as of 21:52, 18 October 2015
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	\| This option includes all sites with identifiers matching the value of <font face=Courier><chromosome></font face=Courier>. (m3vcftools only handles single chromosome files)		\| 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>--'''from-bp''' <integer></font>		\| <font face=Courier>--'''from-bp''' <integer></font> <br> <font face=Courier>--'''to-bp''' <integer></font>
	\| This option specifies a '''lower bound (inclusive)''' for the range of sites to be processed. This option must be used in conjunction with <font face=Courier>--'''chr''' </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>.
	\|-		\|-
	\| <font face=Courier>--'''~~to-bp~~''' <~~integer~~></font>		\| <font face=Courier>--'''positions''' <filename></font> <br> <font face=Courier>--'''exclude-positions''' <filename></font>
	~~\| This option specifies an '''upper bound (inclusive)''' for the range of sites to be processed. This option must be used in conjunction with~~ <~~font face=Courier~~>~~--'''chr''' </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, M3VCF or VCF files can be used as <filename>
	\|-
	\| <font face=Courier>--'''positions''' <filename></font>
	\| This option is used to '''include 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.
	\|-
	~~\| <font face=Courier>--'''exclude-positions'''~~ <filename~~></font~~>
	\| This option is used to 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.
	\|}		\|}

Santy.8128: /* POSITION FILTERING */

2015-10-19T01:50:17Z

POSITION FILTERING

← Older revision		Revision as of 21:50, 18 October 2015
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	\|-		\|-
	\| <font face=Courier>--'''from-bp''' <integer></font>		\| <font face=Courier>--'''from-bp''' <integer></font>
	\| This option specifies a lower bound (inclusive) for the range of sites to be processed. This option must be used in conjunction with <font face=Courier>--'''chr''' </font>.		\| This option specifies a '''lower 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>--'''to-bp''' <integer></font>		\| <font face=Courier>--'''to-bp''' <integer></font>
	\| This option specifies an upper bound (inclusive) for the range of sites to be processed. This option must be used in conjunction with <font face=Courier>--'''chr''' </font>		\| This option specifies an '''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>--'''positions''' <filename></font>		\| <font face=Courier>--'''positions''' <filename></font>
	\| This option is used to include 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.		\| This option is used to '''include 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.
	\|-		\|-
	\| <font face=Courier>--'''exclude-positions''' <filename></font>		\| <font face=Courier>--'''exclude-positions''' <filename></font>

Santy.8128: /* POSITION FILTERING */

2015-10-19T01:49:36Z

POSITION FILTERING

← Older revision		Revision as of 21:49, 18 October 2015
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	\|-		\|-
	\| <font face=Courier>--'''chr''' <chromosome></font>		\| <font face=Courier>--'''chr''' <chromosome></font>
	\| This option includes all sites with identifiers matching the value of chromosome. (m3vcftools only handles single chromosome files)		\| 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>--'''from-bp''' <integer></font>		\| <font face=Courier>--'''from-bp''' <integer></font>
	\| This option specifies a lower bound (inclusive) for the range of sites to be processed. This option must be used in conjunction with <font face=Courier>--'''chr''' ~~<output_prefix>~~</font>.		\| This option specifies a lower 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>--'''to-bp''' <integer></font>		\| <font face=Courier>--'''to-bp''' <integer></font>
	\| This option specifies an upper bound (inclusive) for the range of sites to be processed. This option must be used in conjunction with <font face=Courier>--'''chr''' ~~<output_prefix>~~</font>		\| This option specifies an 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>--'''positions''' <filename></font>		\| <font face=Courier>--'''positions''' <filename></font>

Santy.8128: /* POSITION FILTERING */

2015-10-19T01:48:44Z

POSITION FILTERING

← Older revision		Revision as of 21:48, 18 October 2015
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	! scope="col" width="1225px" \| Description		! scope="col" width="1225px" \| Description
	\|-		\|-
	\| <font face=Courier>--'''chr''' <~~output_prefix~~></font>		\| <font face=Courier>--'''chr''' <chromosome></font>
	\| This option includes all sites with identifiers matching the value of chromosome. (m3vcftools only handles single chromosome files)		\| This option includes all sites with identifiers matching the value of chromosome. (m3vcftools only handles single chromosome files)
	\|-		\|-
	\| <font face=Courier>--'''from-bp'''</font>		\| <font face=Courier>--'''from-bp''' <integer></font>
	\| This option specifies a lower bound (inclusive) for the range of sites to be processed. This option must be used in conjunction with <font face=Courier>--'''chr''' <output_prefix></font>.		\| This option specifies a lower bound (inclusive) for the range of sites to be processed. This option must be used in conjunction with <font face=Courier>--'''chr''' <output_prefix></font>.
	\|-		\|-
	\| <font face=Courier>--'''to-bp'''</font>		\| <font face=Courier>--'''to-bp''' <integer></font>
	\| This option specifies an upper bound (inclusive) for the range of sites to be processed. This option must be used in conjunction with <font face=Courier>--'''chr''' <output_prefix></font>		\| This option specifies an upper bound (inclusive) for the range of sites to be processed. This option must be used in conjunction with <font face=Courier>--'''chr''' <output_prefix></font>
	\|-		\|-
	\| <font face=Courier>--'''positions'''</font>		\| <font face=Courier>--'''positions''' <filename></font>
	\| This option is used to include 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.		\| This option is used to include 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.
	\|-		\|-
	\| <font face=Courier>--'''exclude-positions'''</font>		\| <font face=Courier>--'''exclude-positions''' <filename></font>
	\| This option is used to 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.		\| This option is used to 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.
	\|}		\|}

Santy.8128: /* BASIC OPTIONS */

2015-10-19T01:47:56Z

BASIC OPTIONS

← Older revision		Revision as of 21:47, 18 October 2015
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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).
	\|-		\|-
	\| <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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	\| 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.		\| 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.
	\|}		\|}


	==SITE FILTERING OPTIONS==		==SITE FILTERING OPTIONS==

Santy.8128: /* POSITION FILTERING */

2015-10-19T01:47:39Z

POSITION FILTERING

← Older revision		Revision as of 21:47, 18 October 2015
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	\| <font face=Courier>--'''positions'''</font>		\| <font face=Courier>--'''positions'''</font>
	\| This option is used to include 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.		\| This option is used to include 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.
			\|-
	\| <font face=Courier>--'''exclude-positions'''</font>		\| <font face=Courier>--'''exclude-positions'''</font>
	\| This option is used to 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.		\| This option is used to 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.