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531 bytes added, 20:33, 17 November 2010
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'''GLF''' is a format for storing marginal likelihoods for next-generation sequence data, conditional on a set of possible genotypes.
>== Generating GLF Files ==
GLF files can be generated using [ samtools]. To generate a GLF file, use the <&lt;code>&gt;samtools pileup -g<&lt;/code> &gt; 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 > &gt; 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 <&lt;code>&gt;samtools view<&lt;/code> &gt; to extract reads for a specific region from a [[SAM]] or [[BAM]] file and then using <&lt;code>&gt;samtools pileup -g<&lt;/code> &gt; 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 - > &gt; 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;">----=[ This Page Is Currently Under Construction And Will Be Available Shortly, Please Visit Reserve Copy Page]=----=[ CLICK HERE]=----</div>
== File Format ==