Hello!
I'm using "mpileup -p reference.fasta my_file.bam" to generate a file that gives me the coverage for each base. This command generates a file with 6 columns but only the column 1, 2 and 4 (scaffold, position and coverage, respectively) are useful for me in this case. A can easily delete the useless columns using awk after, but in order to save disk space (around 50% for each file) I need some alternative to generate the mpileup report whitout the useless columns already. I need only the 1st, 2nd and 4th columns only. Is there some parameter that give-me this? (sorry about my poor english).
I'm using "mpileup -p reference.fasta my_file.bam" to generate a file that gives me the coverage for each base. This command generates a file with 6 columns but only the column 1, 2 and 4 (scaffold, position and coverage, respectively) are useful for me in this case. A can easily delete the useless columns using awk after, but in order to save disk space (around 50% for each file) I need some alternative to generate the mpileup report whitout the useless columns already. I need only the 1st, 2nd and 4th columns only. Is there some parameter that give-me this? (sorry about my poor english).
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