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I am performing a GWAS analysis and try to understand the influence of the minor allele count filter.Setting the filter to 1 % gave me this plot and I am confused about the same -log10 pvalues around ~ 3.8 which shows a strange pattern (many dots in one line with same value).

enter image description here

If I increase the filter to 6 % the dots in a line disappear but I loose also some significant SNPs:

enter image description here

Sample are about 77000 SNP positions (barley), unimputed from GWAS (all NaNs removed). GWAS was performed with 200 phenotype samples.

How to interpret the dots in a line?

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  • $\begingroup$ I updated my question. $\endgroup$
    – snowflake
    Aug 21 '20 at 6:33
  • $\begingroup$ Thanks. How many samples and what organism? I assume this is a snp chip? $\endgroup$
    – winni2k
    Aug 21 '20 at 6:44
  • $\begingroup$ Barley with 200 phenotypes. $\endgroup$
    – snowflake
    Aug 21 '20 at 7:04
  • $\begingroup$ There seems to be something wrong with the Manhattan plots: snps from different chromosomes are overlapping? For example, green does can be found inside the region for red dots. $\endgroup$
    – winni2k
    Aug 21 '20 at 7:23
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This looks like genotyping failed for some samples. It's unclear from the op whether the genotyping data was controlled for quality, but I would recommend performing sample QC.

On a side note: in human gwas with imputed snps, I would expect to see clusters of significant snps as a sign that the significant snps are not an artifact. In the op there are some single significant snps. This might be a sign that those significant snps are artifacts. There are also some snps that form clusters and therefore look more promising.

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