RMA Hunter

`header`

Chr Position Ref Alt ID Gene Corrected
Substitution
Corrected predictions Corrected AFs Corrected
RMA GT
AD
PROVEAN Polyphen2 SIFT 1000G ExAC ESP

`header`

Chr Position Ref Alt ID Gene Annotated
type
Corrected
type
Corrected
AFs
Corrected
RMA GT
Variant
GT
Corrected
RMA AD
Variant
AD
1000G ExAC ESP
`h`
`0``1``2``3``4``5``7` `15` `14` `17` `16` `19` `18` `9` `10` `11` `21` `23`/`22`
`56`
`0``1``2``3``4``5` `6` `21``7` `22` `8` `9` `10` `28` `27` `25`/`26` `23`/`24`
`56`

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Analyze specific gene set

To analyze only specific genes of interest, please enter a list of genes (separate with comma or a newline):

RMA false negative

Major
A A
Sample
C C
Reference
A RMA
Standard annotation:
C → A (AF 0.99)
reported sample GT: 0/0
Corrected annotation:
A → C (AF 0.01)
reported sample GT: 1/1

RMA false positive

Major
A A
Sample
A A
Reference
C RMA
Standard annotation:
C → A (AF 0.99)
reported sample GT: 1/1
Corrected annotation:
A → C (AF 0.01)
reported sample GT: 0/0

Variant misclassification

Major
TCG TCG
Sample
TGG TGG
Reference
TCA SNP           RMA
Standard annotation:
Ser → STOP
Corrected annotation:
Ser → Trp
SNP GT: 1/1
Corrected RMA GT: 0/0

← return back (reset all) Analyze specific gene set

If you notice any bugs or inconsistencies please do not hesitate to contact us at predeus@bioinf.me or yury.barbitoff@gmail.com.

This is RMA Hunter — a web-based tool to systematically analyze and correct reference minor alleles in variant calling data. The tool provides a complete list of all false-positive and false-negative RMAs, as well as same-codon variants that switch type due to the presence of RMA. All variants are annotated with correct pathogenicity predictions and reference allele frequencies.

To start, please upload your VCF file and (for exome sequencing or target sequencing assays) a BED-file containing enrichment intervals. To analyze only specific genes of interest, please enter a list of genes (separate with comma or a newline) in the box provided.

Downloads:
You may also download the data files describing RMA and RMA-codon variants in the form of VCF and CSV files: Data_Files.zip

Please cite the tool as:
Barbitoff Y.A., Bezdvornykh I.V., Serebryakova E.A., Glotov A.S., Glotov O.S. and Predeus A.V.
Catching hidden variation: Systematic correction of reference minor alleles in clinical variant calling. (2017)