PMC:5420355 / 7845-8358 JSONTXT

{"project":"2_test","denotations":[{"id":"28475857-27485037-2044934","span":{"begin":74,"end":76},"obj":"27485037"},{"id":"28475857-20980556-2044935","span":{"begin":187,"end":189},"obj":"20980556"},{"id":"28475857-25017105-2044936","span":{"begin":263,"end":265},"obj":"25017105"},{"id":"28475857-26315209-2044937","span":{"begin":292,"end":294},"obj":"26315209"},{"id":"28475857-26315209-2044938","span":{"begin":413,"end":415},"obj":"26315209"}],"text":"Variant Calling\nWe used the OpEx v1.0 pipeline to perform variant calling.18 We converted raw data to FASTQs using CASAVA v.1.8.2 with default settings. The OpEx v1.0 pipeline uses Stampy19 to map to the human reference genome, Picard to flag duplicates, Platypus20 to call variants, and CAVA21 to provide consistent annotation of variants with the HGVS-compliant CSN (Clinical Sequencing Notation) standard v1.0.21 The transcript information for variant annotation for the 14 relevant genes are given in Table 1."}