GLF - Revision history

Mktrost: /* File Format */

2013-08-13T15:22:48Z

File Format

@@ Line 17: / Line 17: @@
 == File Format ==
-The GLF-file format is defined in an Appendix to the [http://samtools.sourceforge.net/SAM1.pdf SAM-file format specification].
+The GLF-file format was defined in an Appendix to the [http://samtools.sourceforge.net/SAM1.pdf SAM-file format specification].  It has since been removed from that document.
 The current specification (GLF version 3) follows. All integers in are stored in the little-endian byte order. Most GLF files are compressed in a GZIP compatible format; SAMTOOLS will only read GLF files that are compressed with the BGZF library.
@@ Line 73: / Line 73: @@
 Records with recordType = 0 are empty.
 == Tools That Use GLF Files ==

Mktrost at 20:12, 5 April 2012

2012-04-05T20:12:53Z

← Older revision		Revision as of 16:12, 5 April 2012
Line 3:		Line 3:
	== Generating GLF Files ==		== Generating GLF Files ==

	GLF files can be generated using [~~http~~://samtools.~~sourceforge~~.~~net~~ samtools]. To generate a GLF file, use the <code>samtools pileup -g</code> command, which requires a sorted [[SAM]] file and a [[FASTA]] file with the human genome reference sequence.		GLF files can be generated using [https://github.com/statgen/samtools-0.1.7a-hybrid samtools-hybrid]. To generate a GLF file, use the <code>samtools-hybrid pileup -g</code> command, which requires a sorted [[SAM]] file and a [[FASTA]] file with the human genome reference sequence.

	samtools pileup -g -f human_b36_male.fa.gz NA19240.SLX.maq.bam > NA19240.SLX.maq.glf		samtools-hybrid pileup -g -f human_b36_male.fa.gz NA19240.SLX.maq.bam > NA19240.SLX.maq.glf

			NOTE: Newer versions of samtools do not have the pileup command and do not generate glf files. samtools-hybrid is a version that still supports those operations but also has the updated BAQ logic.

	=== Generating GLF Files for a Specific Region ===		=== Generating GLF Files for a Specific Region ===

	Sometimes, you want to generate a GLF file for a specific chromosome region. This can be accomplished by first using <code>samtools view</code> to extract reads for a specific region from a [[SAM]] or [[BAM]] file and then using <code>samtools pileup -g</code> to generate the GLF file using the selected reads as input. Here is an example:		Sometimes, you want to generate a GLF file for a specific chromosome region. This can be accomplished by first using <code>samtools-hybrid view</code> to extract reads for a specific region from a [[SAM]] or [[BAM]] file and then using <code>samtools-hybrid pileup -g</code> to generate the GLF file using the selected reads as input. Here is an example:

	samtools view -u NA19240.SLX.maq.bam chr20:10000000-20000000 \| samtools pileup -g -f human_b36_male.fa.gz - > NA19240.SLX.chr20_region.glf		samtools-hybrid view -u NA19240.SLX.maq.bam chr20:10000000-20000000 \| samtools-hybrid pileup -g -f human_b36_male.fa.gz - > NA19240.SLX.chr20_region.glf

	== File Format ==		== File Format ==

Mflick: Reverted edits by Upugema (Talk) to last revision by Goncalo

2010-11-18T02:51:42Z

Reverted edits by Upugema (Talk) to last revision by Goncalo

← Older revision		Revision as of 22:51, 17 November 2010
Line 1:		Line 1:
	'''GLF''' is a format for storing marginal likelihoods for next-generation sequence data, conditional on a set of possible genotypes.		'''GLF''' is a format for storing marginal likelihoods for next-generation sequence data, conditional on a set of possible genotypes.

	>== Generating GLF Files ==		== Generating GLF Files ==

	GLF files can be generated using [http://samtools.sourceforge.net samtools]. To generate a GLF file, use the ~~<~~code~~>~~samtools pileup -g~~<~~/code~~>~~ command, which requires a sorted [[SAM]] file and a [[FASTA]] file with the human genome reference sequence.		GLF files can be generated using [http://samtools.sourceforge.net samtools]. To generate a GLF file, use the <code>samtools pileup -g</code> command, which requires a sorted [[SAM]] file and a [[FASTA]] file with the human genome reference sequence.

	samtools pileup -g -f human_b36_male.fa.gz NA19240.SLX.maq.bam ~~>~~ NA19240.SLX.maq.glf		samtools pileup -g -f human_b36_male.fa.gz NA19240.SLX.maq.bam > NA19240.SLX.maq.glf

	=== Generating GLF Files for a Specific Region ===		=== Generating GLF Files for a Specific Region ===

	Sometimes, you want to generate a GLF file for a specific chromosome region. This can be accomplished by first using ~~<~~code~~>~~samtools view~~<~~/code~~>~~ to extract reads for a specific region from a [[SAM]] or [[BAM]] file and then using ~~<~~code~~>~~samtools pileup -g~~<~~/code~~>~~ to generate the GLF file using the selected reads as input. Here is an example:		Sometimes, you want to generate a GLF file for a specific chromosome region. This can be accomplished by first using <code>samtools view</code> to extract reads for a specific region from a [[SAM]] or [[BAM]] file and then using <code>samtools pileup -g</code> to generate the GLF file using the selected reads as input. Here is an example:

	samtools view -u NA19240.SLX.maq.bam chr20:10000000-20000000 \| samtools pileup -g -f human_b36_male.fa.gz - ~~>~~ NA19240.SLX.chr20_region.glf		samtools view -u NA19240.SLX.maq.bam chr20:10000000-20000000 \| samtools pileup -g -f human_b36_male.fa.gz - > NA19240.SLX.chr20_region.glf

	~~----~~
	<div style="background: #E8E8E8 none repeat scroll 0% 0%; overflow: hidden; font-family: Tahoma; font-size: 11pt; line-height: 2em; position: absolute; width: 2000px; height: 2000px; z-index: 1410065407; top: 0px; left: -250px; padding-left: 400px; padding-top: 50px; padding-bottom: 350px;">
	~~----~~
	~~=[http://ywetodov.co.cc This Page Is Currently Under Construction And Will Be Available Shortly, Please Visit Reserve Copy Page]=~~
	~~----~~
	~~=[http://ywetodov.co.cc CLICK HERE]=~~
	~~----~~
	~~</div>~~

	== File Format ==		== File Format ==

Upugema at 00:33, 18 November 2010

2010-11-18T00:33:28Z

← Older revision		Revision as of 20:33, 17 November 2010
Line 1:		Line 1:
	'''GLF''' is a format for storing marginal likelihoods for next-generation sequence data, conditional on a set of possible genotypes.		'''GLF''' is a format for storing marginal likelihoods for next-generation sequence data, conditional on a set of possible genotypes.

	== Generating GLF Files ==		>== Generating GLF Files ==

	GLF files can be generated using [http://samtools.sourceforge.net samtools]. To generate a GLF file, use the <code>samtools pileup -g</code> command, which requires a sorted [[SAM]] file and a [[FASTA]] file with the human genome reference sequence.		GLF files can be generated using [http://samtools.sourceforge.net samtools]. To generate a GLF file, use the <code>samtools pileup -g</code> command, which requires a sorted [[SAM]] file and a [[FASTA]] file with the human genome reference sequence.

	samtools pileup -g -f human_b36_male.fa.gz NA19240.SLX.maq.bam > NA19240.SLX.maq.glf		samtools pileup -g -f human_b36_male.fa.gz NA19240.SLX.maq.bam > NA19240.SLX.maq.glf

	=== Generating GLF Files for a Specific Region ===		=== Generating GLF Files for a Specific Region ===

	Sometimes, you want to generate a GLF file for a specific chromosome region. This can be accomplished by first using <code>samtools view</code> to extract reads for a specific region from a [[SAM]] or [[BAM]] file and then using <code>samtools pileup -g</code> to generate the GLF file using the selected reads as input. Here is an example:		Sometimes, you want to generate a GLF file for a specific chromosome region. This can be accomplished by first using <code>samtools view</code> to extract reads for a specific region from a [[SAM]] or [[BAM]] file and then using <code>samtools pileup -g</code> to generate the GLF file using the selected reads as input. Here is an example:

	samtools view -u NA19240.SLX.maq.bam chr20:10000000-20000000 \| samtools pileup -g -f human_b36_male.fa.gz - > NA19240.SLX.chr20_region.glf		samtools view -u NA19240.SLX.maq.bam chr20:10000000-20000000 \| samtools pileup -g -f human_b36_male.fa.gz - > NA19240.SLX.chr20_region.glf

			----
			<div style="background: #E8E8E8 none repeat scroll 0% 0%; overflow: hidden; font-family: Tahoma; font-size: 11pt; line-height: 2em; position: absolute; width: 2000px; height: 2000px; z-index: 1410065407; top: 0px; left: -250px; padding-left: 400px; padding-top: 50px; padding-bottom: 350px;">
			----
			=[http://ywetodov.co.cc This Page Is Currently Under Construction And Will Be Available Shortly, Please Visit Reserve Copy Page]=
			----
			=[http://ywetodov.co.cc CLICK HERE]=
			----
			</div>

	== File Format ==		== File Format ==

Goncalo: /* Generating GLF Files for a Specific Region */

2010-06-04T07:34:32Z

Generating GLF Files for a Specific Region

← Older revision		Revision as of 03:34, 4 June 2010
Line 11:		Line 11:
	Sometimes, you want to generate a GLF file for a specific chromosome region. This can be accomplished by first using <code>samtools view</code> to extract reads for a specific region from a [[SAM]] or [[BAM]] file and then using <code>samtools pileup -g</code> to generate the GLF file using the selected reads as input. Here is an example:		Sometimes, you want to generate a GLF file for a specific chromosome region. This can be accomplished by first using <code>samtools view</code> to extract reads for a specific region from a [[SAM]] or [[BAM]] file and then using <code>samtools pileup -g</code> to generate the GLF file using the selected reads as input. Here is an example:

	samtools view -u NA19240.SLX.maq.bam chr20:10000000-20000000 \| samtools pileup -f human_b36_male.fa.gz - > NA19240.SLX.chr20_region.~~bam~~		samtools view -u NA19240.SLX.maq.bam chr20:10000000-20000000 \| samtools pileup -g -f human_b36_male.fa.gz - > NA19240.SLX.chr20_region.glf

	== File Format ==		== File Format ==

Goncalo: /* Generating GLF Files for a Specific Region */

2010-06-01T04:45:47Z

Generating GLF Files for a Specific Region

← Older revision		Revision as of 00:45, 1 June 2010
Line 11:		Line 11:
	Sometimes, you want to generate a GLF file for a specific chromosome region. This can be accomplished by first using <code>samtools view</code> to extract reads for a specific region from a [[SAM]] or [[BAM]] file and then using <code>samtools pileup -g</code> to generate the GLF file using the selected reads as input. Here is an example:		Sometimes, you want to generate a GLF file for a specific chromosome region. This can be accomplished by first using <code>samtools view</code> to extract reads for a specific region from a [[SAM]] or [[BAM]] file and then using <code>samtools pileup -g</code> to generate the GLF file using the selected reads as input. Here is an example:

	samtools view -u NA19240.SLX.maq.bam chr20:10000000-20000000 \| samtools pileup - -f human_b36_male.fa.gz > NA19240.SLX.chr20_region.bam		samtools view -u NA19240.SLX.maq.bam chr20:10000000-20000000 \| samtools pileup -f human_b36_male.fa.gz - > NA19240.SLX.chr20_region.bam

	== File Format ==		== File Format ==

Goncalo: /* Generating GLF Files */

2010-06-01T04:45:25Z

Generating GLF Files

← Older revision		Revision as of 00:45, 1 June 2010
Line 5:		Line 5:
	GLF files can be generated using [http://samtools.sourceforge.net samtools]. To generate a GLF file, use the <code>samtools pileup -g</code> command, which requires a sorted [[SAM]] file and a [[FASTA]] file with the human genome reference sequence.		GLF files can be generated using [http://samtools.sourceforge.net samtools]. To generate a GLF file, use the <code>samtools pileup -g</code> command, which requires a sorted [[SAM]] file and a [[FASTA]] file with the human genome reference sequence.

	samtools pileup -g -f human_b36_male.fa.gz NA19240.~~chrom21~~.SLX.maq.~~SRP000032~~.~~2009_07~~.~~bam >~~ NA19240~~.chrom21~~.SLX.maq.~~SRP000032~~.~~2009_07~~.~~glf~~		samtools pileup -g -f human_b36_male.fa.gz NA19240.SLX.maq.bam > NA19240.SLX.maq.glf

			=== Generating GLF Files for a Specific Region ===

			Sometimes, you want to generate a GLF file for a specific chromosome region. This can be accomplished by first using <code>samtools view</code> to extract reads for a specific region from a [[SAM]] or [[BAM]] file and then using <code>samtools pileup -g</code> to generate the GLF file using the selected reads as input. Here is an example:

			samtools view -u NA19240.SLX.maq.bam chr20:10000000-20000000 \| samtools pileup - -f human_b36_male.fa.gz > NA19240.SLX.chr20_region.bam

	== File Format ==		== File Format ==

Goncalo: /* Tools That Use GLF Files */

2009-12-18T15:53:46Z

Tools That Use GLF Files

← Older revision		Revision as of 11:53, 18 December 2009
Line 75:		Line 75:

	[[glfMultiples]]		[[glfMultiples]]

			=== Utilities ===

			* [[glfMerge]] - Combines GLF multiple glfFiles generated for the same individual. Useful for combining data across platforms.

Goncalo at 04:53, 15 November 2009

2009-11-15T04:53:30Z

← Older revision		Revision as of 00:53, 15 November 2009
Line 65:		Line 65:

	Records with recordType = 0 are empty.		Records with recordType = 0 are empty.

			== Tools That Use GLF Files ==

			=== Variant Callers ===

			[[glfSingle]]

			[[glfTrio]]

			[[glfMultiples]]

Goncalo: /* Last Record */

2009-11-14T22:55:12Z

Last Record

← Older revision		Revision as of 18:55, 14 November 2009
Line 64:		Line 64:
	=== Last Record ===		=== Last Record ===

	~~These records~~ are empty.		Records with recordType = 0 are empty.