https://www.popgen.dk/angsd/index.php?action=history&feed=atom&title=Vcf Vcf - Revision history 2026-04-27T21:01:55Z Revision history for this page on the wiki MediaWiki 1.40.1 https://www.popgen.dk/angsd/index.php?title=Vcf&diff=3181&oldid=prev Isin: /* Output files */ 2023-06-21T21:53:55Z <p><span dir="auto"><span class="autocomment">Output files</span></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 23:53, 21 June 2023</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28">Line 28:</td> <td colspan="2" class="diff-lineno">Line 28:</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>&lt;/pre&gt;</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>&lt;/pre&gt;</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>&lt;/div&gt;</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>&lt;/div&gt;</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>Notice that the <del style="font-weight: bold; text-decoration: none;">sampleDI </del>simply an ind followed by <del style="font-weight: bold; text-decoration: none;">and </del>integer. These <del style="font-weight: bold; text-decoration: none;">relate </del>to the samples <del style="font-weight: bold; text-decoration: none;">form </del>the -b filelist</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>Notice that the <ins style="font-weight: bold; text-decoration: none;">sampleID is </ins>simply an ind followed by <ins style="font-weight: bold; text-decoration: none;">an </ins>integer. These <ins style="font-weight: bold; text-decoration: none;">correspond </ins>to the samples <ins style="font-weight: bold; text-decoration: none;">from </ins>the <ins style="font-weight: bold; text-decoration: none;">`</ins>-b filelist<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> </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>==References==</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>==References==</div></td></tr> </table> Isin https://www.popgen.dk/angsd/index.php?title=Vcf&diff=3161&oldid=prev Thorfinn at 10:32, 23 May 2022 2022-05-23T10:32:26Z <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 12:32, 23 May 2022</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l29">Line 29:</td> <td colspan="2" class="diff-lineno">Line 29:</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>&lt;/div&gt;</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>&lt;/div&gt;</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>Notice that the sampleDI simply an ind followed by and integer. These relate to the samples form the -b filelist</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>Notice that the sampleDI simply an ind followed by and integer. These relate to the samples form the -b filelist</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;"></del></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;">==NB==</del></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;">This is still very beta, please let us know if it doesn't work. I'm especially concerned about the scaling of gls...</del></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;"></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;"><div>==References==</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>==References==</div></td></tr> </table> Thorfinn https://www.popgen.dk/angsd/index.php?title=Vcf&diff=2408&oldid=prev Thorfinn: /* NB */ 2015-04-27T15:00:45Z <p><span dir="auto"><span class="autocomment">NB</span></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 17:00, 27 April 2015</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l31">Line 31:</td> <td colspan="2" class="diff-lineno">Line 31:</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>==NB==</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>==NB==</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>This is still very beta, please let us know <del style="font-weight: bold; text-decoration: none;">i</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>This is still very beta, please let us know <ins style="font-weight: bold; text-decoration: none;">if it doesn't work. I'm especially concerned about the scaling of gls...</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> </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>==References==</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>==References==</div></td></tr> </table> Thorfinn https://www.popgen.dk/angsd/index.php?title=Vcf&diff=2407&oldid=prev Thorfinn: /* Output files */ 2015-04-27T14:53:26Z <p><span dir="auto"><span class="autocomment">Output files</span></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 16:53, 27 April 2015</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28">Line 28:</td> <td colspan="2" class="diff-lineno">Line 28:</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>&lt;/pre&gt;</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>&lt;/pre&gt;</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>&lt;/div&gt;</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>&lt;/div&gt;</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;">&lt;/div&gt;</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>Notice that the <ins style="font-weight: bold; text-decoration: none;">sampleDI </ins>simply an <ins style="font-weight: bold; text-decoration: none;">ind followed by and </ins>integer<ins style="font-weight: bold; text-decoration: none;">. These relate to </ins>the <ins style="font-weight: bold; text-decoration: none;">samples form </ins>the <ins style="font-weight: bold; text-decoration: none;">-b filelist</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>Notice that the <del style="font-weight: bold; text-decoration: none;">family id </del>simply an <del style="font-weight: bold; text-decoration: none;">incrementing </del>integer<del style="font-weight: bold; text-decoration: none;">, and that </del>the <del style="font-weight: bold; text-decoration: none;">SNPid is </del>the <del style="font-weight: bold; text-decoration: none;">genomic position.</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>==NB==</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>==NB==</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>This is still very beta, please let us know i</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>This is still very beta, please let us know i</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>==References==</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>==References==</div></td></tr> </table> Thorfinn https://www.popgen.dk/angsd/index.php?title=Vcf&diff=2406&oldid=prev Thorfinn: Created page with "Newer versions of angsd (master 27april2015) supports basic vcf output. This will only include gl and gp tags which can be useful for certain external programs Supply ;-doVc..." 2015-04-27T14:47:03Z <p>Created page with &quot;Newer versions of angsd (master 27april2015) supports basic vcf output. This will only include gl and gp tags which can be useful for certain external programs Supply ;-doVc...&quot;</p> <p><b>New page</b></p><div>Newer versions of angsd (master 27april2015) supports basic vcf output. This will only include gl and gp tags which can be useful for certain external programs<br /> <br /> Supply<br /> ;-doVcf 1<br /> <br /> Which is simply a wrapper around -gl -dopost -domajorminor -domaf. <br /> <br /> <br /> ==Example==<br /> A full example commandline is given below:<br /> <br /> &lt;pre&gt;<br /> ./angsd -b list.list -dovcf 1 -gl 1 -dopost 1 -domajorminor 1 -domaf 1 -snp_pval 1e-6<br /> &lt;/pre&gt;<br /> <br /> ==Output files==<br /> This will generate a vcf file called angsdput.vcf.gz<br /> &lt;div class=&quot;toccolours mw-collapsible mw-collapsed&quot;&gt;<br /> angsdput.vcf.gz<br /> &lt;pre class=&quot;mw-collapsible-content&quot;&gt;<br /> ##FORMAT=&lt;ID=GL,Number=G,Type=Float,Description=&quot;scaled Genotype Likelihoods (these are really llh eventhough they sum to one)&quot;&gt;<br /> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind0 ind1 ind2 ind3 ind4 ind5 ind6 ind7 ind8 ind9 ind10 ind11 ind12 ind13 ind14 ind15 ind16 ind17 ind18 ind19 ind20 ind21 ind22 ind23 ind24 ind25 ind26 ind27 ind28 ind29 ind30 ind31 ind32<br /> 1 14000202 . G A . PASS . GL:GP 0.013409,0.986591,0.000001:0.009959,0.990038,0.000003 0.532745,0.394297,0.072957:0.333333,0.333333,0.333333 0.532745,0.394297,0.072957:0.333333,0.333333,0.333333 0.729804,0.270070,0.000126:0.666110,0.333052,0.000839 0.532745,0.394297,0.072957:0.333333,0.333333,0.333333 0.013409,0.986589,0.000003:0.009959,0.990026,0.000015 0.843814,0.156129,0.000057:0.799685,0.199918,0.000397 0.003405,0.996582,0.000013:0.002523,0.997410,0.000068 0.915318,0.084679,0.000003:0.888870,0.111106,0.000025 0.843862,0.156138,0.000000:0.800003,0.199997,0.000000 0.001243,0.728985,0.269772:0.000420,0.333191,0.666388 0.955789,0.044211,0.000000:0.941178,0.058822,0.000000 0.843860,0.156137,0.000003:0.799987,0.199993,0.000020 0.000001,0.999999,0.000000:0.000001,0.999999,0.000000 0.824856,0.152621,0.022523:0.689947,0.172484,0.137569 0.701963,0.259767,0.038270:0.526842,0.263419,0.209740 0.532745,0.394297,0.072957:0.333333,0.333333,0.333333 0.004272,0.995611,0.000117:0.003164,0.996204,0.000632 0.532745,0.394297,0.072957:0.333333,0.333333,0.333333 0.021392,0.791754,0.186854:0.008712,0.435643,0.555645 0.843681,0.156104,0.000215:0.798816,0.199700,0.001484 0.729804,0.270070,0.000126:0.666110,0.333052,0.000839 0.002698,0.996374,0.000928:0.001990,0.993012,0.004997 0.977395,0.022605,0.000000:0.969698,0.030302,0.000000 0.532745,0.394297,0.072957:0.333333,0.333333,0.333333 0.002152,0.997847,0.000002:0.001593,0.998397,0.000010 0.915213,0.084669,0.000118:0.888149,0.111016,0.000835 0.032903,0.965645,0.001452:0.024405,0.967730,0.007865 0.000006,0.999994,0.000000:0.000005,0.999995,0.000000 0.701963,0.259767,0.038270:0.526842,0.263419,0.209740 0.843846,0.156135,0.000019:0.799896,0.199971,0.000133 0.907127,0.083921,0.008952:0.835380,0.104420,0.060201 0.332066,0.644735,0.023200:0.241926,0.634652,0.123421<br /> 1 14000873 . G A . PASS . 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