The strand bias here means the genotyped infered from info presented by the forward strand and the reverse strand disagress. For example，
read depths data at a position after mapping could be
ref 20 33
alt 19 0
, which shows strong strand bias.
My question is that how come this happen? I think there might be 4 possible causes:
1 the sample itself does not strickly base paired
2 exome capture bias ( how could this happen? )
3 sequencing error(how could this happen?)
4 mapping error
Am I right? Any comments is welcome!