hi all :
I am using BWA with default parameters, and i get my alignement file (.sam).
Now with samtools, i am trying to call SNPs with pileup command :
and i got :
.
chrY 186 T T 75 0 36 20 G,,.....,,,.,,..,-1g,., !eb^]$`%^d\aae^Y%UIB
.
.
chrY 300 A A 42 0 37 6 .+2TC,..., !cb`_S
i noticed that many lines contain the same base in the reference and the read sequence.
is that's normal ? if yes what is that means , and if not, what is probably the explanation or the solution.
thanks
I am using BWA with default parameters, and i get my alignement file (.sam).
Now with samtools, i am trying to call SNPs with pileup command :
and i got :
.
chrY 186 T T 75 0 36 20 G,,.....,,,.,,..,-1g,., !eb^]$`%^d\aae^Y%UIB
.
.
chrY 300 A A 42 0 37 6 .+2TC,..., !cb`_S
i noticed that many lines contain the same base in the reference and the read sequence.
is that's normal ? if yes what is that means , and if not, what is probably the explanation or the solution.
thanks