Question: Reasons For Low Ts/Tv Ratio
0
gravatar for Les Ander
8.7 years ago by
Les Ander110
United States
Les Ander110 wrote:

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

exome snp • 3.4k views
ADD COMMENTlink modified 8.2 years ago by Lars Juhl Jensen11k • written 8.7 years ago by Les Ander110
1

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

ADD REPLYlink written 8.7 years ago by Sean Davis26k

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

ADD REPLYlink written 8.7 years ago by lh332k

@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.

ADD REPLYlink written 8.7 years ago by Les Ander110
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