Scripps Genome ADVISER | Annotation and Distributed Variant Interpretation Server

Errors Description

We try to provide result files for every single variant uploaded through the web however there are times when input files don't follow our format. Some formating errors we are able to correct and other times we don't know how the user wants us to translate the variants. In those case we provide a error file as well the option of submitting a reduced set of correct variants for annotation by following the steps in the email we send you.

Errors we can fix:

1. Negative strand - if some variants are negative strand variants we will transform them into positive strand variants; 'neg_strand' denotes a negative to positive strand correction for a variant
2. Reference and alternate alleles are reversed - we compare each variant to the hg19 reference genome and reverse the reference and alternate alleles if needed; 'ref_alt_rev' denotes a reversal of the reference and alternate columns for a particular line


Errors we can not fix:

1. Number of fields in some columns - verify that each line has 8 columns, tab separated with the chromosome column (2) is in the format "chrX". If the 8th column contains no data, substitute a dash or a period as a place holder.
2. Invalid chromosome identifiers - ensure the chromosomes are formatted as 'chrX' only regular chromosomes 1-22,X,Y are accepted.
3. Malformed Insert variants - ensure the alternate allele only contains valid bases [A,C,G,T];
4. Malformed Deletion variants - ensure the reference allele contains only valid bases and aligns to the appropriate reference genome; ensure the reference allele is correct with respect to the target genome at the specified coordinates.
5. Malformed SNP variants - ensure the coordinates are correctly formatted, end = start + 1; ensure both the reference and alternate allele contain valid bases [A,C,G,T]; ensure the reference allele is correct with respect to the target genome at the specified coordinates.
6. Malformed delins (indel) found - ensure the coordinates are correctly formatted end = start + lenght of the reference allele; ensure both the reference and alternate allele contain valid bases [A,C,G,T]; ensure the reference allele is correct with respect to the target genome at the specified coordinates.
7. Unknown variant type - only use valid variant types - snp / ins / del / delins; remove invalid lines from input file;
8. Invalid base found in a reference or alternate allele - ensure both the reference and alternate allele contain valid bases [A,C,G,T]; verify source data.
9. Illegal starting coordinate - verify all starting coordinates are integers, also the start <= end; verify source data; remove invalid lines from input file.
10. Illegal ending coordinate - verify all starting coordinates are integers, also the start <= end; verify source data; remove invalid lines from input file.
11. Matching reference and alternative allele - verify source data; remove invalid lines from input file.




Scripps Genome ADVISER | Annotation and Distributed Variant Interpretation Server