https://www.limswiki.org/index.php?action=history&feed=atom&title=File%3AFig1_Tsai_JofPersMed2016_6-1.png 2026-04-05T18:14:11Z Revision history for this page on the wiki MediaWiki 1.36.1 https://www.limswiki.org/index.php?title=File:Fig1_Tsai_JofPersMed2016_6-1.png&diff=28517&oldid=prev 2016-11-21T21:21:00Z

<p>Added summary.</p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 21:21, 21 November 2016</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td colspan="2"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">==Summary==</ins></div></td></tr> <tr><td colspan="2"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">{{Information</ins></div></td></tr> <tr><td colspan="2"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">|Description='''Figure 1.''' WGS Alignment and Variant Calling Pipeline. There are multiple entry points to our pipeline where it can be re-triggered due to system failures or outside datasets. Standard processing of genome data from the Illumina Clinical Services Laboratory starts at the top entry point. From there, FASTQ sequences are aligned to the reference hg19 genome using the burrows-wheeler aligner (bwa). Since the alignment is computationally intensive, we divided the sequence files into smaller files. The alignments, known as “raw” BAM files in our pipeline, are processed through a series of steps prior to variant calling. The “final” BAM file is the resulting file after removing PCR artifacts, local indel realignment, and base quality recalibration. This is used as the input file to the variant caller portion of the pipeline. Variant calling happens in two phases, where the variants are identified and then their quality scores are recalibrated in the final VCF file.</ins></div></td></tr> <tr><td colspan="2"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">|Source={{cite journal |journal=Journal of Personalized Medicine |title=Bioinformatics workflow for clinical whole genome sequencing at Partners HealthCare Personalized Medicine |author=Tsai, E.A.; Shakbatyan, R.; Evan, J.; Rossetti, P.; Graham, C.; Sharma, H.; Lin, C.-F., Lebo, M.S. |volume=6 |issue=1 |pages=12 |year=2016 |doi=10.3390/jpm6010012 |pmid=26927186 |pmc=PMC4810391}}</ins></div></td></tr> <tr><td colspan="2"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">|Author=Tsai, E.A.; Shakbatyan, R.; Evan, J.; Rossetti, P.; Graham, C.; Sharma, H.; Lin, C.-F., Lebo, M.S.</ins></div></td></tr> <tr><td colspan="2"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">|Date=2016</ins></div></td></tr> <tr><td colspan="2"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">|Permission=[http://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International]</ins></div></td></tr> <tr><td colspan="2"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">}}</ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Licensing ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Licensing ==</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{{cc-by-4.0}}</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{{cc-by-4.0}}</div></td></tr> <!-- diff cache key limswiki:diff::1.12:old-28516:rev-28517 --> </table>

Shawndouglas https://www.limswiki.org/index.php?title=File:Fig1_Tsai_JofPersMed2016_6-1.png&diff=28516&oldid=prev 2016-11-21T21:17:12Z

<p></p> <p><b>New page</b></p><div>== Licensing ==<br /> {{cc-by-4.0}}</div>

Shawndouglas