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Old 09-10-2018, 03:49 AM   #1
weehzer
Junior Member
 
Location: Austria

Join Date: Mar 2017
Posts: 6
Question SNP calling on samples sequenced with different technology

Hi,
is it possible to compare SNPs from alignments of different samples, whereas the samples weren't sequenced on the same illumina platform?
Let's say some were sequenced with HiSeq 2x100, some with MySeq 2x300 and some others with NextSeq 2x150.
We were discussing this issue recently, as we found a paper saying that all of these technologies have (slightly) different sorts of sequencing errors and rates.

However, I also read papers were they used sequenced samples together with simulated reads from a reference genome for analysis. So I guess it should be fine.

Any comment and thoughts on the issue are highly appreciated.

Thanks a lot & kind regards!
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different error rates, illumina, snp calling, technologies

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