Reasons For Low Ts/Tv Ratio

Question

[Les Ander]

Hello, I've done human exome capture (with Truseq) and sequenced with HiSeq. I found that the ts/tv ratio is ~1.6 for the dozen exomes that I sequenced. I am not sure why this is and wonder if this is a bioinformatics issue (i.e. filtering) or the exome capture issue. I used the same mutation calling pipeline for my earlier exomes using Agilent SureSelect and there my ts/tv ratio was ~3 thanks Les

[Sean Davis]

What kind of samples? Tumors or normals? What type of filtering did you do?

[lh3]

Ts/tv is for the exonic regions only or whole-genome?

[Les Ander]

@Sean_Davis: These are for normal samples. I have only kept variants supported by at least 4 alleles with base quality of 30+; @lh3: These are for exonic regions.