Gelabel -check.marker error

Question

[krp0001]

Hello @all

I working on genome wide association analysis with GenABEL, of my fungal genome data, with more than a million SNPs.

I am able to do descriptives.trait and descriptives.marker scan of my genotype and phenotype and descriptive.scan of raw data.

But when i go quality check of my data with check.marker i get bellow error

gwadata <- load.gwaa.data(phenofile="phenomean.dat",genofile="quali-fil-scaf58.raw")
ids loaded...
marker names loaded...
chromosome data loaded...
map data loaded...
allele coding data loaded...
strand data loaded...
genotype data loaded...
snp.data object created...
assignment of gwaa.data object FORCED; X-errors were not checked!
qc1 <- check.marker(gwadata)
Excluding people/markers with extremely low call rate...
1019387 markers and 29 people in total
0 people excluded because of call rate < 0.1 
958 markers excluded because of call rate < 0.1 
Passed: 1018429 markers and 29 people

RUN 1 
1018429 markers and 29 people in total
231574 (22.73835%) markers excluded as having low (<8.62069%) minor allele frequency
332801 (32.67788%) markers excluded because of low (<95%) call rate
1018429 (100%) markers excluded because they are out of HWE (FDR <0.2)

 Error in .local(x, i, j, ..., drop) : j out of range (== 0) In
 addition: Warning message: In max(j) : no non-missing arguments to
 max; returning -Inf``

Could you help me with this. I will be helpful if you please also share a script to use after quality check of the data to analyse (descriptive.marker and descriptive.scan) for further GWAS analysis

Thank you Best regards KRP

Answer 1

[david.ashbrook]

Did you ever get an answer to this? I've got a similar problem.

edit: I got around this by running the QC multiple times on subsets of 1000000 markers, creating new gwaa.data file for each of these rounds of QC, and then using the merge.gwaa.data function to merge these. Only markers, not people, were removed from my QC, so hopefully this wont have any effect on downstream association.