Changes

From Genome Analysis Wiki
Jump to: navigation, search

GLF

3 bytes added, 03:34, 4 June 2010
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 -g -f human_b36_male.fa.gz - > NA19240.SLX.chr20_region.bamglf
== File Format ==

Navigation menu