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
Thanks
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