Hi,
I am wondering if there's utility in samtools that can modify reads flag in a
bam file? I am currently piping into and out of awk, e.g.:
samtools view a.bam | awk '{OFS="\t"; $2=or($2,0x40); print}' | samtools view
-bT ref.fa -o b.bam -
which is quite slow compared with a "native" solution, if one is justified to
draw similarities from comparing "samtools view -q 10" and "samtools view | awk
'$5>=10'".
Any suggestion outside samtools would also be welcome!
Many thanks,
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