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                    5.9 years ago
        bioguy24
        
    
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    230
    Using samtools 1.9 to calculate overall read depth per base of targets in a bed then reads at q30 in a bam. Is there a way to combine these or a tool/script that will do this more optimally to produce the final output? Thank you :).
samtools depth -a -b <bed> -aa <bam>
samtools depth -q 30 -a -b <bed> <bam>
bed
chr10   8097600 80976   xxx_AGRN.1_1    0   +   AGRN
chr10   8097580 8097680 xxx_AGRN_1  0   +   AGRN
chr10   8097580 8097700 xxx_AGRN_2  0   +   AGRN
current out command one
chr10   8097609 247
chr10   8097610 256
chr10   8097611 258
current out command two
chr10   8097609 196
chr10   8097610 228
chr10   8097611 245
then I merge the two with awk to get the overall reads per base in target matched with the q30, and gene (final output)
chr10   8097609 247 196 AGRN
chr10   8097610 256 228 AGRN
chr10   8097611 258 245 AGRN