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. 2020 Jul 7;11:813. doi: 10.3389/fpls.2020.00813

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Copyright © 2020 Haas, Fernandez-Pozo, Meyberg, Perroud, Göttig, Stingl, Saint-Marcoux, Langdale and Rensing.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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RNA-seq SNP calling pipeline. Part (A) of this pipeline was previously published (Perroud et al., 2018). The additional SNP calling branch (B) on the right side starts with removing read duplications, using Samtools package “markdup” and continues with the GATK toolbox for SNP calling (C). The last steps of this pipeline are post processing steps like SnpEff and EMBOSS restrict together with UNIX shell scripts. This figure has been modified based on a figure published in The Plant Journal (Perroud et al., 2018; https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.13940).