I'm using BWA 0.7.12. sampe to align paired end reads. I would like to get the alignment score, but can't find AS tag in the SAM files. Same thing happens when using samse for single end reads.
Where did the AS tag go? Is there another way to get the alignment score? (I need it for a downstream analysis and can't use the mapping quality).
Thanks. I understand that for bwa mem the AS tag is printed, but what about sampe ad samse? My reads are ~50bp long and according to bwa manual the recommended algorithm is BWA-backtrack (sampe/samse).