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Old 10-19-2015, 10:25 PM   #1
alpha2zee
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Location: New York

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Default Mutation/variant calling with cell-line sequencing data

I plan to use whole exome sequencing data to identify mutation events induced in a human cell-line following treatment with various reagents.

I expect the reagent to cause single nucleotide changes (transition/transversion) at hundreds and perhaps thousands of genome positions and at a low rate (may be 0.5%-1%). I will compare exome sequences of control and reagent-treated cells (triplicates).

I have a reasonable idea of the various variant calling or mutation detection methods and pipelines that exist for data from human tissues (normal or cancer) but I am not sure how suitable they are for data from cell-lines. E.g., the cell-line that I am using is hypotriploid and has undergone a lot of sequence variations over time compared to the genome of the individual from whom it was derived.

I will appreciate any thought or suggestion on this. Thanks.
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