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Does the pull down kit matter for alignment?

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!

exome alignment
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updated by Biostar Biostar • written by dwells • dwells

1 answer

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

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written by WouterDeCoster WouterDeCoster

Ok, great news, thanks a lot!

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written by dwells • dwells

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