I found bam-readcount to be very useful for further filtering SNVs and Indels.
However, I do not understand a few fields of bam-readcount outputs and cannot find any other information regarding some of the fields other than the github page of bam-readcount.
(1) num_q2_containing_reads → number of reads with q2 runs at the 3’ end (2) avg_distance_to_q2_start_in_q2_reads → average distance of position (as fraction of unclipped read length) to the start of the q2 run
Does anyone know what the two fields listed above mean (from bam-readcount)? What does "q2" mean?