invalid genotypes in cross

[Madi Shoken]

Hi, 

I get this error,

In check_cross2(output) : 443597 invalid genotypes in crossIn

How can i solve this error?

thanks, 

Madi

[Karl Broman]

In your control file you should have lines like the following, which define the genotype codes:

genotypes: 

   AA: 1 

   AB: 2 

   BB: 3

The genotype data need to be all using these three codes (in this case, AA, AB, BB).

karl

[Karl Broman]

The error means that there are 443,597 genotypes in your genotype data files that are not one of those genotype codes, and not one of the missing value codes (defined by na.strings).

karl

[Madi Shoken]

Yes i know that, all my genotype data using these three codes (such as AA, AB, BB).

I even wrote down the genotype codes in my write_control_file.

ma_control_file_madi <- file.path("C:/Users/shoke/OneDrive/Документы", "madi.yaml")
write_control_file(ma_control_file_madi,
                   crosstype = "riself",
                   geno_file = "madi_geno.csv",
                   gmap_file = "madi_gmap.csv",
                   pheno_file = "madi_pheno.csv",
                   alleles = c("AA", "BB"),
                   geno_codes = c("AA" = 1, "AB" = 2, "BB" = 3),
                   na.strings = "NN",
                   sep = ",",
                   geno_transposed = T,
                   overwrite = TRUE)

but I still have this error.

среда, 15 мая 2024 г. в 18:40:12 UTC+5, Karl Broman:

[Karl Broman]

Sorry; I was wrong. It doesn't have to do with the genotypes not matching the genotype codes, but rather that you have something like heterozygotes in recombinant inbred lines.

Could you say more about the nature of your data? What is the cross type?

karl

[Madi Shoken]

The data comes from wheat F8 RILs obtained from cross of two parents and genotyped with 43K SNP markers.

We have four such mapping populations. Initially I did all QC (omitting clones, homozygous and distorted markers etc) for the four populations simultaneously (merged maps). Once high quality map obtained, now I want to conduct QTL analysis for each population separately. So I devided my QC-ed map to four. When read that map again faced this issue. What to understand how warning this warning message is.

ср, 15 мая 2024 г., 20:26 Karl Broman <kbr...@gmail.com>:

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[Madi Shoken]

Sorry there was a mistake, I excluded monomorphic markers and not homozygous.

Thanks,

Madi

ср, 15 мая 2024 г., 20:41 Madi Shoken <shoke7...@gmail.com>:

[Madi Shoken]

Hi Karl,

ma_control_file_madi <- file.path("C:/Users/shoke/OneDrive/Документы", "madi.yaml")
write_control_file(ma_control_file_madi,
                   crosstype = "riself",
                   geno_file = "madi_geno.csv",
                   gmap_file = "madi_gmap.csv",
                   pheno_file = "madi_pheno.csv",

                   geno_codes = list(AA = 1, AB = 2, BB = 3),

                   alleles = c("AA","BB"),

                   na.strings= c("-", "NN"),
                   sep = ";",

                   geno_transposed = T,
                   overwrite = TRUE)

Tsel_map <- read_cross2("Tsel.yaml")

In check_cross2(output) : 443597 invalid genotypes in crossIn

Check my data and code, otherwise we still connot solve this warning.

Or can we ignore this warning? because my genotypes consist of AA, AB, BB.

Thanks,

Madi

среда, 15 мая 2024 г. в 20:25:58 UTC+5, Karl Broman:

[Karl Broman]

You can ignore the warning. The heterozygote genotypes will be treated as missing.

To avoid the warning, you could change the geno_codes and na.strings in the control file:

    geno_codes=list(AA=1, BB=3),

    na.strings=c("-", "NN", "AB"),

karl