Question: Does the pull down kit matter for alignment?
0
gravatar for dwells
14 months ago by
dwells0
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.

Thanks!

alignment exome • 379 views
ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 14 months ago by dwells0
3
gravatar for WouterDeCoster
14 months ago by
Belgium
WouterDeCoster42k 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 14 months ago by WouterDeCoster42k

Ok, great news, thanks a lot!

ADD REPLYlink written 14 months ago by dwells0
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