Our collaborator, Dr. Laura Riva, indicates a criteria to filter out variant in her paper.

“Second, we removed base substitutions with a median alignment score of mutation-reporting reads <140 and complex indels."

This leads to my research of what it is.

Firstly, there is an explanation of alignment score by the Broad Institute

grep -v "@" seq_aln.sam | awk -F"\t" 'BEGIN{print "flag\toccurrences"} {a[$2]++} END{for(i in a)print i"\t"a[i]}'