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5.0 years ago
bioguy24
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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