Question: Meaning of TOP/BOTTOM strand and QC implications
gravatar for ognjen011
2.1 years ago by
ognjen011200 wrote:

I've found a post explaining strand designations for some Illumina systems:

So the way they explain it is some local designation which is robust to reference genome build rearrangements. What confuses me is the supplementary of the following paper:

In Table 1 they list this as exclusion criteria on Illumina 370CNV:

Call rate <97%, HWE p<1-6, MAF <1%, Mishap p<1-9, A/T and G/C SNPs, Mismatches between Illumina, dbSNP and/or HapMap position

Why would anyone exclude A/T and G/C SNPs? (Also, what is mishap?)

Thanks in advance!

snp illumina • 914 views
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