Changes

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 ==