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Old 10-21-2010, 11:49 AM   #4
Location: Texas

Join Date: May 2010
Posts: 13

Thanks for the info.
Here is what I have tried so far to view the file for a given sample:
samtools view filename.bam chr:start-end

For non SNP positions, I am getting the base coverage using the following command:
samtools view filename.bam chr:start-end |wc -l

Sometimes the actual position is missing when I grep it and ~50 bases around it are printed. My question is how can I trust the wc -l value for a position if that position itself is missing in the BAM file?

Last edited by unagaswamy; 10-21-2010 at 12:37 PM.
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