Computational protocol: Isolated Congenital Anosmia and CNGA2 Mutation

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Protocol publication

[…] DNA libraries were processed and analyzed using the Roche Sequencing Solutions (Bina Technologies version 2.7.9) whole-exome analysis workflow with default settings. Briefly, libraries were mapped with BWA mem 0.7.5 software to human genome (hg19 version), and then realigned around indels with GATK IndelRealigner. Next, base recalibration was performed with GATK BaseRecalibrator taking into account the read group, quality scores, and cycle and context covariates. Variants were called with GATK HaplotypeCaller with the parameters–variant_index_ type LINEAR–variant_index_parameter 128000. VQSR was used to recalibrate the variants, first with GATK VariantRecalibrator and then ApplyRecalibration. Variant filtering and annotation was done using Golden Helix VarSeq Version 1.1 software (http://goldenhelix.com/products/VarSeq/). After importing the variant call files (gVCF files) of each member of the family, the variants were organized by pedigree. Using the 1000 genomes variant frequencies (phase 1), the Exome Aggregation Consortium (ExAC) variant frequency database version 0.3 (Cambridge, MA), and the NHLBI Exome Sequencing Project (https://esp.gs.washington.edu/drupal/) V2 Exome Variant Frequencies, rare variants (minor allele frequency <1%) were filtered. Variants were then classified according to whether they were deemed to be coding. […]

Pipeline specifications

Software tools BWA, GATK, VarSeq
Application WES analysis
Organisms Mus musculus, Homo sapiens