From Genome Analysis Wiki
Jump to navigationJump to search
482 bytes added
, 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 == |