q30 using multicovergebam greater the target length
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5.0 years ago
bioguy24 ▴ 230

I am using bedtools 2.29 multibam to output the bases in a bed that are at a minimum of q30 and am would like to output the total reads as well. Is this possible in one command? Column 4 is the target length and column 6 is the q30. Thank you :).

file.bed

chr9    135766724   135772151   5428    +   TSC1
chr9    135772560   135772742   183 +   TSC1
chr9    135772799   135773007   209 +   TSC1

command

multiBamCov -q 30 -bams sorted.bam -bed file.bed  > q30

output

chr9    135766724   135772151   5428    +   TSC1    2846
chr9    135772560   135772742   183 +   TSC1    644
chr9    135772799   135773007   209 +   TSC1    529
multibam coverage • 622 views
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