using filter in Samtools

[emilyjia2000]

Hi,

I have exome sequencing data and would like to do the variant call, when I used fastQC and found out that the "per base sequence quality" drops down very fast at the end of the sequence read. Does anybody know if Samtools could help fix it? or any other solutions?

Thanks a lot,

[swbarnes2]

Samtools can't fix poor data quality.

But most software, like samtools, carries nucleotide quality scores throughout the process, so the quality score of a potential variant will take into account the quality score of each individual nucleotide involved.