TY - JOUR
T1 - MACARON
T2 - A python framework to identify and re-annotate multi-base affected codons in whole genome/exome sequence data
AU - Khan, Waqasuddin
AU - Varma Saripella, Ganapathi
AU - Ludwig, Thomas
AU - Cuppens, Tania
AU - Thibord, Florian
AU - Génin, Emmanuelle
AU - Deleuze, Jean Francois
AU - Trégouët, David Alexandre
N1 - Publisher Copyright:
© The Author(s) 2018.
PY - 2018/10/1
Y1 - 2018/10/1
N2 - Summary: Predicted deleteriousness of coding variants is a frequently used criterion to filter out variants detected in next-generation sequencing projects and to select candidates impacting on the risk of human diseases. Most available dedicated tools implement a base-to-base annotation approach that could be biased in presence of several variants in the same genetic codon. We here proposed the MACARON program that, from a standard VCF file, identifies, re-annotates and predicts the amino acid change resulting from multiple single nucleotide variants (SNVs) within the same genetic codon. Applied to the whole exome dataset of 573 individuals, MACARON identifies 114 situations where multiple SNVs within a genetic codon induce an amino acid change that is different from those predicted by standard single SNV annotation tool. Such events are not uncommon and deserve to be studied in sequencing projects with inconclusive findings.
AB - Summary: Predicted deleteriousness of coding variants is a frequently used criterion to filter out variants detected in next-generation sequencing projects and to select candidates impacting on the risk of human diseases. Most available dedicated tools implement a base-to-base annotation approach that could be biased in presence of several variants in the same genetic codon. We here proposed the MACARON program that, from a standard VCF file, identifies, re-annotates and predicts the amino acid change resulting from multiple single nucleotide variants (SNVs) within the same genetic codon. Applied to the whole exome dataset of 573 individuals, MACARON identifies 114 situations where multiple SNVs within a genetic codon induce an amino acid change that is different from those predicted by standard single SNV annotation tool. Such events are not uncommon and deserve to be studied in sequencing projects with inconclusive findings.
UR - http://www.scopus.com/inward/record.url?scp=85054674079&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/bty382
DO - 10.1093/bioinformatics/bty382
M3 - Article
C2 - 29726922
AN - SCOPUS:85054674079
SN - 1367-4803
VL - 34
SP - 3396
EP - 3398
JO - Bioinformatics
JF - Bioinformatics
IS - 19
ER -
