Question: Does the pull down kit matter for alignment?
gravatar for dwells
6 months ago by
dwells0 wrote:

I have a set of bams for which the sequence was generated many years ago using one of the Agilent SureSelect2 pull down kit. My understanding is that this kit was made during the "hg19" time. I would like to realign these bams to hg38 to match up with our best practices. I know how to do this, but I am wondering, are there any caveats and issues with the use of a target set that was presumably derived from hg19.


alignment exome • 254 views
ADD COMMENTlink modified 9 weeks ago by Biostar ♦♦ 20 • written 6 months ago by dwells0
gravatar for WouterDeCoster
6 months ago by
WouterDeCoster37k wrote:

While this kit was made using hg19 coordinates, its probes are based on sequences and the alignment should not be affected by genome build.

ADD COMMENTlink written 6 months ago by WouterDeCoster37k

Ok, great news, thanks a lot!

ADD REPLYlink written 6 months ago by dwells0
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