fundamental strand bias in sequence data

[kingsalex]

Does anyone else see fundamental strand bias in many mapped read positions. That is, for exome sequencing I see both reference allele and variant allele in one particular stand only, can be either + or - strand, for many cases, as if only one strand has been aligned or sequenced at those positions? I am using casva 1.8 to align and then resulting BAM files processed with samtools (sort and mpileup) and varscan.

Thanks

[Lluc]

I'm not familiar with exome sequencing, but I would suspect that the strategy used to enrich the sample in exons may have introduced that bias.

[m_two]

In any capture data the regions farthest from the probes tend to have single stranded coverage if the read length is shorter than the insert length.