From Genome Analysis Wiki
Jump to navigationJump to search
No change in size
, 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 == |