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Issue with converting VCF to genlight #25
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Thanks for reporting the bug Emily |
Sorry for the long delay Emily, the problem is outside radiator. Currently working to resolve this. It's related to how freeBayes/dDocent generate the VCF (not ideal...below the full details). In the vcf header for the format field you have these info:
So anyone reading the file would expect 10 values for each individuals: The FORMAT column is okay and output 8 values expected: But some software/packages are using what's described in the header to parse the VCF file, but that's not the only problem, because removing those lines in the VCF doesn't solve the error and the genotypes are still not outputted (the GT field in the VCF)... more later... |
The INFO fields have the same problem:
but only those are found for each SNPs (44 described and expected, 42 found in the data):
|
correction: genotypes are parsed correctly... |
weird stuff in your vcf... e.g. line 83, column 17 (sample ID: BRSPHaw_024) or
The genotype is missing or was erased and the remaining values shows 3 values for allele depth (AD) and 6 values for GL. Your vcf is multi-allelic (haplotypes) but that marker is supposed to be biallelic (REF/ALT : C/T)... reminds me of the genepop format where, with time, people started generating variants of the file format which became increasingly difficult to parse correctly! |
should work now |
Hi Thierry,
Thanks for all your work with radiator! I'm getting an error when trying to convert a VCF file (v4.2, biallelic, produced by FreeBayes) to genlight. This is the command used:
genomic_converter(data="~/Downloads/TotalRawSNPsHISEQ.biallelic.vcf.recode.vcf", output='genlight', vcf.metadata = TRUE, strata="~/Downloads/strata.tsv")
And the output/error message:
And here is my sessionInfo():
Any input/help would be much appreciated!
Emily
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