diff --git a/docs/images/sarek_subway.png b/docs/images/sarek_subway.png index 99390eb2a6..37defa92fa 100644 Binary files a/docs/images/sarek_subway.png and b/docs/images/sarek_subway.png differ diff --git a/docs/images/sarek_subway.svg b/docs/images/sarek_subway.svg index 758c4c50d5..ae51a85965 100644 --- a/docs/images/sarek_subway.svg +++ b/docs/images/sarek_subway.svg @@ -2,23 +2,23 @@ + inkscape:export-filename="/Users/monarchy/Projects/sarek_paper/sarek_subway.png" + inkscape:export-xdpi="600" + inkscape:export-ydpi="600" + xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" + xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" + xmlns="http://www.w3.org/2000/svg" + xmlns:svg="http://www.w3.org/2000/svg" + xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:cc="http://creativecommons.org/ns#" + xmlns:dc="http://purl.org/dc/elements/1.1/"> @@ -40,14 +40,14 @@ inkscape:pagecheckerboard="false" inkscape:document-units="mm" showgrid="true" - inkscape:zoom="0.70638235" - inkscape:cx="597.40122" - inkscape:cy="403.23134" - inkscape:window-width="1920" - inkscape:window-height="1007" - inkscape:window-x="0" - inkscape:window-y="0" - inkscape:window-maximized="1" + inkscape:zoom="1.4142136" + inkscape:cx="549.77552" + inkscape:cy="118.44039" + inkscape:window-width="2560" + inkscape:window-height="1027" + inkscape:window-x="1440" + inkscape:window-y="25" + inkscape:window-maximized="0" inkscape:current-layer="layer4" width="211mm" fit-margin-top="0" @@ -57,13 +57,175 @@ lock-margins="false" units="mm" inkscape:showpageshadow="false" - inkscape:deskcolor="#d1d1d1"> + inkscape:deskcolor="#d1d1d1" + showguides="false"> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -811,6 +973,42 @@ inkscape:export-filename="/Users/monarchy/Projects/Coding/sarek/docs/images/sarek_subway.png" inkscape:export-xdpi="90" inkscape:export-ydpi="90"> + + + + vcf vcf + vcf vcf + vcf vcf + vcf vcf + vcf vcf + vcf vcf + + fas fas + - + - variant calling + pre-processing + annotation + variant calling: SNPs, Indels, SV, CNV, MSI + variant calling Adapted from: Fellows Yates, James A., et al. PeerJ 9 (2021). @@ -2118,31 +2388,31 @@ tiddit mutect2 ascat msisensorpro controlfreec cnvkit vcf vcf + vcf vcf + cra cra + freebayes manta strelka2 - 3.0 + style="font-style:normal;font-variant:normal;font-weight:500;font-stretch:normal;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro Medium';stroke-width:1.00002">3.0.1 + Example analysis pathways + + + + + + + + + + + + + + + + mpileup mpileup + +