http://genome.sph.umich.edu/w/index.php?action=history&feed=atom&title=Understanding_VerifyBamID_output 2026-09-27T19:05:12Z Revision history for this page on the wiki MediaWiki 1.43.1 http://genome.sph.umich.edu/w/index.php?title=Understanding_VerifyBamID_output&diff=6637&oldid=prev 2013-03-04T20:48:08Z

<p><span class="autocomment">Expected Output from verifyBamID</span></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 16:48, 4 March 2013</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3">Line 3:</td> <td colspan="2" class="diff-lineno">Line 3:</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;"><br></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;"><br></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>There will be four types of files produced by [[verifyBamID]]</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>There will be four types of files produced by [[verifyBamID]]</div></td></tr> <tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* '''*.selfSM''' : '''Main output file containing the contamination estimate'''. If you are only interested in checking sample contamination, check the 'FREEMIX' column for genotype-free estimate of contamination, and 'CHIPMIX' column for contamination estimates with external genotypes (if <del style="font-weight: bold; text-decoration: none;">available</del>)</div></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>* '''*.selfSM''' : '''Main output file containing the contamination estimate'''. If you are only interested in checking sample contamination, check the 'FREEMIX' column for genotype-free estimate of contamination, and 'CHIPMIX' column for contamination estimates with external genotypes (if <ins style="font-weight: bold; text-decoration: none;">provided</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>* *.selfRG : Same output to .*selfRG, but separated by readGroup (which might be helpful for library-level examination)</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>* *.selfRG : Same output to .*selfRG, but separated by readGroup (which might be helpful for library-level examination)</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>* *.depthSM : The depth distribution of reads covering the marker position of the input VCF, across all readGroups.</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>* *.depthSM : The depth distribution of reads covering the marker position of the input VCF, across all readGroups.</div></td></tr> </table>

Hmkang http://genome.sph.umich.edu/w/index.php?title=Understanding_VerifyBamID_output&diff=6636&oldid=prev 2013-03-04T20:47:29Z

<p><span class="autocomment">Expected Output from verifyBamID</span></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 16:47, 4 March 2013</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3">Line 3:</td> <td colspan="2" class="diff-lineno">Line 3:</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;"><br></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;"><br></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>There will be four types of files produced by [[verifyBamID]]</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>There will be four types of files produced by [[verifyBamID]]</div></td></tr> <tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* ''*.selfSM'' : ''Main output file containing the contamination estimate''. If you are only interested in checking sample contamination, check the 'FREEMIX' column for genotype-free estimate of contamination, and 'CHIPMIX' column for contamination estimates with external genotypes (if available)</div></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>''*.selfSM<ins style="font-weight: bold; text-decoration: none;">'</ins>'' : <ins style="font-weight: bold; text-decoration: none;">'</ins>''Main output file containing the contamination estimate<ins style="font-weight: bold; text-decoration: none;">'</ins>''. If you are only interested in checking sample contamination, check the 'FREEMIX' column for genotype-free estimate of contamination, and 'CHIPMIX' column for contamination estimates with external genotypes (if available)</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>* *.selfRG : Same output to .*selfRG, but separated by readGroup (which might be helpful for library-level examination)</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>* *.selfRG : Same output to .*selfRG, but separated by readGroup (which might be helpful for library-level examination)</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>* *.depthSM : The depth distribution of reads covering the marker position of the input VCF, across all readGroups.</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>* *.depthSM : The depth distribution of reads covering the marker position of the input VCF, across all readGroups.</div></td></tr> </table>

Hmkang http://genome.sph.umich.edu/w/index.php?title=Understanding_VerifyBamID_output&diff=6635&oldid=prev 2013-03-04T20:47:15Z

<p><span class="autocomment">Expected Output from verifyBamID</span></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 16:47, 4 March 2013</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3">Line 3:</td> <td colspan="2" class="diff-lineno">Line 3:</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;"><br></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;"><br></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>There will be four types of files produced by [[verifyBamID]]</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>There will be four types of files produced by [[verifyBamID]]</div></td></tr> <tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* *.selfSM : Main output file containing the contamination estimate. If you are only interested in checking sample contamination, check the 'FREEMIX' column for genotype-free estimate of contamination, and 'CHIPMIX' column for contamination estimates with external genotypes (if available)</div></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>*.selfSM<ins style="font-weight: bold; text-decoration: none;">'' </ins>: <ins style="font-weight: bold; text-decoration: none;">''</ins>Main output file containing the contamination estimate<ins style="font-weight: bold; text-decoration: none;">''</ins>. If you are only interested in checking sample contamination, check the 'FREEMIX' column for genotype-free estimate of contamination, and 'CHIPMIX' column for contamination estimates with external genotypes (if available)</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>* *.selfRG : Same output to .*selfRG, but separated by readGroup (which might be helpful for library-level examination)</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>* *.selfRG : Same output to .*selfRG, but separated by readGroup (which might be helpful for library-level examination)</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>* *.depthSM : The depth distribution of reads covering the marker position of the input VCF, across all readGroups.</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>* *.depthSM : The depth distribution of reads covering the marker position of the input VCF, across all readGroups.</div></td></tr> </table>

Hmkang http://genome.sph.umich.edu/w/index.php?title=Understanding_VerifyBamID_output&diff=6634&oldid=prev 2013-03-04T20:46:37Z

<p></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 16:46, 4 March 2013</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 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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>=<del style="font-weight: bold; text-decoration: none;">Example VerifyBamID </del>Output=</div></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;">= Expected </ins>Output <ins style="font-weight: bold; text-decoration: none;">from verifyBamID </ins>=<ins style="font-weight: bold; text-decoration: none;">=</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></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;">This section explains the expected output from [[verifyBamID]] software. See [[VerifyBamID#Interpreting_output_files|VerifyBamID output documentation]] for more details.</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;"><br></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;"><br></td></tr> <tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Verify BAM ID produces the following </del>files<del style="font-weight: bold; text-decoration: none;">:</del></div></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;">There will be four types of </ins>files <ins style="font-weight: bold; text-decoration: none;">produced by [[verifyBamID]]</ins></div></td></tr> <tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* *.<del style="font-weight: bold; text-decoration: none;">genoCheck</del>.<del style="font-weight: bold; text-decoration: none;">depthRG</del></div></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;">selfSM : Main output file containing the contamination estimate</ins>. <ins style="font-weight: bold; text-decoration: none;">If you are only interested in checking sample contamination, check the 'FREEMIX' column for genotype-free estimate of contamination, and 'CHIPMIX' column for contamination estimates with external genotypes (if available)</ins></div></td></tr> <tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* *.<del style="font-weight: bold; text-decoration: none;">genoCheck</del>.<del style="font-weight: bold; text-decoration: none;">depthSM</del></div></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;">selfRG : Same output to </ins>.<ins style="font-weight: bold; text-decoration: none;">*selfRG, but separated by readGroup (which might be helpful for library-level examination)</ins></div></td></tr> <tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* *.<del style="font-weight: bold; text-decoration: none;">genoCheck</del>.<del style="font-weight: bold; text-decoration: none;">selfRG</del></div></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;">depthSM : The depth distribution of reads covering the marker position of the input VCF, across all readGroups</ins>.</div></td></tr> <tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* *.<del style="font-weight: bold; text-decoration: none;">genoCheck.selfSM</del></div></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;">depthRG : : The depth distribution of reads covering the marker position of the input VCF, per readGroups</ins>.</div></td></tr> <tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">See [[VerifyBamID#Interpreting_output_files|VerifyBamID output documentation]] for more details</del>.</div></td><td colspan="2" class="diff-side-added"></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;"><br></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;"><br></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>== VerifyBamID Tutorial Output ==</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>== VerifyBamID Tutorial Output ==</div></td></tr> </table>

Hmkang http://genome.sph.umich.edu/w/index.php?title=Understanding_VerifyBamID_output&diff=6508&oldid=prev 2013-02-25T03:12:33Z

<p>Created page with &#039;=Example VerifyBamID Output= Verify BAM ID produces the following files: * *.genoCheck.depthRG * *.genoCheck.depthSM * *.genoCheck.selfRG * *.genoCheck.selfSM See [[VerifyBamID…&#039;</p> <p><b>New page</b></p><div>=Example VerifyBamID Output=<br /> <br /> Verify BAM ID produces the following files:<br /> * *.genoCheck.depthRG<br /> * *.genoCheck.depthSM<br /> * *.genoCheck.selfRG<br /> * *.genoCheck.selfSM<br /> <br /> See [[VerifyBamID#Interpreting_output_files|VerifyBamID output documentation]] for more details.<br /> <br /> == VerifyBamID Tutorial Output ==<br /> <br /> The VerifyBamID output from the [[Tutorial: GotCloud| GotCloud Tutorial]] looks like this:<br /> <br /> === HG00096.genoCheck.depthRG ===<br /> <br /> &lt;pre&gt;<br /> #RG DEPTH #SNPs %SNPs %CUMUL<br /> SRR062634 20 0 0.00000 0.00000<br /> SRR062634 19 0 0.00000 0.00000<br /> SRR062634 18 0 0.00000 0.00000<br /> SRR062634 17 0 0.00000 0.00000<br /> SRR062634 16 0 0.00000 0.00000<br /> SRR062634 15 0 0.00000 0.00000<br /> SRR062634 14 0 0.00000 0.00000<br /> SRR062634 13 0 0.00000 0.00000<br /> SRR062634 12 0 0.00000 0.00000<br /> SRR062634 11 0 0.00000 0.00000<br /> SRR062634 10 0 0.00000 0.00000<br /> SRR062634 9 0 0.00000 0.00000<br /> SRR062634 8 0 0.00000 0.00000<br /> SRR062634 7 0 0.00000 0.00000<br /> SRR062634 6 0 0.00000 0.00000<br /> SRR062634 5 1 0.00003 0.00003<br /> SRR062634 4 1 0.00003 0.00006<br /> SRR062634 3 9 0.00025 0.00030<br /> SRR062634 2 22 0.00061 0.00091<br /> SRR062634 1 62 0.00171 0.00262<br /> SRR062634 0 36203 0.99738 1.00000<br /> SRR062635 20 0 0.00000 0.00000<br /> SRR062635 19 0 0.00000 0.00000<br /> SRR062635 18 0 0.00000 0.00000<br /> SRR062635 17 0 0.00000 0.00000<br /> SRR062635 16 0 0.00000 0.00000<br /> SRR062635 15 0 0.00000 0.00000<br /> SRR062635 14 0 0.00000 0.00000<br /> SRR062635 13 0 0.00000 0.00000<br /> SRR062635 12 0 0.00000 0.00000<br /> SRR062635 11 0 0.00000 0.00000<br /> SRR062635 10 0 0.00000 0.00000<br /> SRR062635 9 0 0.00000 0.00000<br /> SRR062635 8 0 0.00000 0.00000<br /> SRR062635 7 0 0.00000 0.00000<br /> SRR062635 6 0 0.00000 0.00000<br /> SRR062635 5 0 0.00000 0.00000<br /> SRR062635 4 0 0.00000 0.00000<br /> SRR062635 3 4 0.00011 0.00011<br /> SRR062635 2 14 0.00039 0.00050<br /> SRR062635 1 65 0.00179 0.00229<br /> SRR062635 0 36215 0.99771 1.00000<br /> SRR062641 20 0 0.00000 0.00000<br /> SRR062641 19 0 0.00000 0.00000<br /> SRR062641 18 0 0.00000 0.00000<br /> SRR062641 17 0 0.00000 0.00000<br /> SRR062641 16 0 0.00000 0.00000<br /> SRR062641 15 0 0.00000 0.00000<br /> SRR062641 14 0 0.00000 0.00000<br /> SRR062641 13 0 0.00000 0.00000<br /> SRR062641 12 0 0.00000 0.00000<br /> SRR062641 11 0 0.00000 0.00000<br /> SRR062641 10 0 0.00000 0.00000<br /> SRR062641 9 0 0.00000 0.00000<br /> SRR062641 8 0 0.00000 0.00000<br /> SRR062641 7 0 0.00000 0.00000<br /> SRR062641 6 0 0.00000 0.00000<br /> SRR062641 5 1 0.00003 0.00003<br /> SRR062641 4 3 0.00008 0.00011<br /> SRR062641 3 8 0.00022 0.00033<br /> SRR062641 2 23 0.00063 0.00096<br /> SRR062641 1 58 0.00160 0.00256<br /> SRR062641 0 36205 0.99744 1.00000<br /> &lt;/pre&gt;<br /> <br /> <br /> === HG00096.genoCheck.depthSM ===<br /> <br /> &lt;pre&gt;<br /> #RG DEPTH #SNPs %SNPs %CUMUL<br /> ALL 20 0 0.00000 0.00000<br /> ALL 19 0 0.00000 0.00000<br /> ALL 18 0 0.00000 0.00000<br /> ALL 17 0 0.00000 0.00000<br /> ALL 16 0 0.00000 0.00000<br /> ALL 15 0 0.00000 0.00000<br /> ALL 14 0 0.00000 0.00000<br /> ALL 13 0 0.00000 0.00000<br /> ALL 12 0 0.00000 0.00000<br /> ALL 11 0 0.00000 0.00000<br /> ALL 10 0 0.00000 0.00000<br /> ALL 9 0 0.00000 0.00000<br /> ALL 8 2 0.00006 0.00006<br /> ALL 7 2 0.00006 0.00011<br /> ALL 6 7 0.00019 0.00030<br /> ALL 5 10 0.00028 0.00058<br /> ALL 4 17 0.00047 0.00105<br /> ALL 3 34 0.00094 0.00198<br /> ALL 2 31 0.00085 0.00284<br /> ALL 1 38 0.00105 0.00388<br /> ALL 0 36157 0.99612 1.00000<br /> &lt;/pre&gt;<br /> <br /> <br /> === HG00096.genoCheck.selfRG ===<br /> <br /> &lt;pre&gt;<br /> #SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT<br /> HG00096 SRR062634 NA 36298 142 0.00 0.00000 40.76 40.76 NA NA NA NA NA NA NA NA NA NA<br /> HG00096 SRR062635 NA 36298 105 0.00 0.00000 38.05 38.05 NA NA NA NA NA NA NA NA NA NA<br /> HG00096 SRR062641 NA 36298 145 0.00 0.00000 43.96 43.96 NA NA NA NA NA NA NA NA NA NA<br /> &lt;/pre&gt;<br /> <br /> <br /> === HG00096.genoCheck.selfSM ===<br /> <br /> &lt;pre&gt;<br /> #SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT<br /> HG00096 ALL NA 36298 392 0.01 0.00000 86.22 86.22 NA NA NA NA NA NA NA NA NA NA<br /> &lt;/pre&gt;<br /> <br /> <br /> === HG00100.genoCheck.depthRG ===<br /> <br /> &lt;pre&gt;<br /> #RG DEPTH #SNPs %SNPs %CUMUL<br /> ERR013140 20 0 0.00000 0.00000<br /> ERR013140 19 0 0.00000 0.00000<br /> ERR013140 18 0 0.00000 0.00000<br /> ERR013140 17 0 0.00000 0.00000<br /> ERR013140 16 0 0.00000 0.00000<br /> ERR013140 15 0 0.00000 0.00000<br /> ERR013140 14 0 0.00000 0.00000<br /> ERR013140 13 0 0.00000 0.00000<br /> ERR013140 12 0 0.00000 0.00000<br /> ERR013140 11 0 0.00000 0.00000<br /> ERR013140 10 0 0.00000 0.00000<br /> ERR013140 9 0 0.00000 0.00000<br /> ERR013140 8 0 0.00000 0.00000<br /> ERR013140 7 0 0.00000 0.00000<br /> ERR013140 6 0 0.00000 0.00000<br /> ERR013140 5 1 0.00003 0.00003<br /> ERR013140 4 2 0.00006 0.00008<br /> ERR013140 3 3 0.00008 0.00017<br /> ERR013140 2 23 0.00063 0.00080<br /> ERR013140 1 44 0.00121 0.00201<br /> ERR013140 0 36225 0.99799 1.00000<br /> ERR016352 20 0 0.00000 0.00000<br /> ERR016352 19 0 0.00000 0.00000<br /> ERR016352 18 0 0.00000 0.00000<br /> ERR016352 17 0 0.00000 0.00000<br /> ERR016352 16 0 0.00000 0.00000<br /> ERR016352 15 0 0.00000 0.00000<br /> ERR016352 14 0 0.00000 0.00000<br /> ERR016352 13 0 0.00000 0.00000<br /> ERR016352 12 0 0.00000 0.00000<br /> ERR016352 11 0 0.00000 0.00000<br /> ERR016352 10 0 0.00000 0.00000<br /> ERR016352 9 0 0.00000 0.00000<br /> ERR016352 8 0 0.00000 0.00000<br /> ERR016352 7 0 0.00000 0.00000<br /> ERR016352 6 0 0.00000 0.00000<br /> ERR016352 5 0 0.00000 0.00000<br /> ERR016352 4 0 0.00000 0.00000<br /> ERR016352 3 0 0.00000 0.00000<br /> ERR016352 2 4 0.00011 0.00011<br /> ERR016352 1 22 0.00061 0.00072<br /> ERR016352 0 36272 0.99928 1.00000&lt;/pre&gt;<br /> <br /> <br /> === HG00100.genoCheck.depthSM ===<br /> <br /> &lt;pre&gt;<br /> #RG DEPTH #SNPs %SNPs %CUMUL<br /> ALL 20 0 0.00000 0.00000<br /> ALL 19 0 0.00000 0.00000<br /> ALL 18 0 0.00000 0.00000<br /> ALL 17 0 0.00000 0.00000<br /> ALL 16 0 0.00000 0.00000<br /> ALL 15 0 0.00000 0.00000<br /> ALL 14 0 0.00000 0.00000<br /> ALL 13 0 0.00000 0.00000<br /> ALL 12 0 0.00000 0.00000<br /> ALL 11 0 0.00000 0.00000<br /> ALL 10 0 0.00000 0.00000<br /> ALL 9 0 0.00000 0.00000<br /> ALL 8 0 0.00000 0.00000<br /> ALL 7 0 0.00000 0.00000<br /> ALL 6 2 0.00006 0.00006<br /> ALL 5 0 0.00000 0.00006<br /> ALL 4 1 0.00003 0.00008<br /> ALL 3 9 0.00025 0.00033<br /> ALL 2 28 0.00077 0.00110<br /> ALL 1 43 0.00118 0.00229<br /> ALL 0 36215 0.99771 1.00000<br /> &lt;/pre&gt;<br /> <br /> <br /> === HG00100.genoCheck.selfSM ===<br /> <br /> &lt;pre&gt;<br /> #SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT<br /> HG00100 ALL NA 36298 142 0.00 0.49991 59.51 60.55 NA NA NA NA NA NA NA NA NA NA<br /> &lt;/pre&gt;<br /> <br /> <br /> === HG00100.genoCheck.selfRG ===<br /> <br /> &lt;pre&gt;<br /> #SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT<br /> HG00100 ERR013140 NA 36298 112 0.00 0.49995 48.17 49.67 NA NA NA NA NA NA NA NA NA NA<br /> HG00100 ERR016352 NA 36298 30 0.00 0.49995 12.52 12.61 NA NA NA NA NA NA NA NA NA NA<br /> &lt;/pre&gt;</div>

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