Unable to convert some variants

[ns3116]

Some variants from the Infinium Global screening Array 24 v2.0 do not convert

Here is the log with the errors, and the corresponding manifest lines.

gtcvcf.log manifest_missing.csv.txt

[KelleyRyanM]

A few comments on the log messages that you observed

• The reference and alternate alleles are not specified directly in the manifest, so this information must be inferred. The inference process involves mapping the source sequence (typically taken from dbSNP) to the genome.
• In rare circumstances, the source sequence may not fully match to the expected location in the genome. In those cases, the program will provide a warning. If the mapping of the source sequence is poor enough such that the reference allele can not be inferred unambiguously, the program will not include the variant in the VCF file. This is only the case for rs111060774.
• Other warning messages indicate that the specific variant does not query the reference allele. Certain multi-nucleotide variants (such as rs63750329) are encoded as single nucleotide variants within the manifest. There is a list of such variants in the downloads available at https://support.illumina.com/array/array_kits/infinium-global-screening-array/downloads.html. The GTCtoVCF program contains an option to use the provided VCF annotation as input to produce appropriate VCF output for these multi-nucleotide variants.