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Mastodon: AboutGet the appKeyboard shortcutsView source codev4.4.0-nightly.2025-03-25

#structuralvariant

1 post1 participant0 posts today
Pierre Lindenbaum<p><a href="https://github.com/yangao07/longcallD" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">github.com/yangao07/longcallD</span><span class="invisible"></span></a> LongcallD is a local-haplotagging-based variant caller designed for detecting small variants and structural variants (SVs) using long-read sequencing data. It supports both PacBio HiFi and Oxford Nanopore reads. <a href="https://genomic.social/tags/sv" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sv</span></a> <a href="https://genomic.social/tags/structuralvariant" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>structuralvariant</span></a> <a href="https://genomic.social/tags/calling" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>calling</span></a> <a href="https://genomic.social/tags/mapping" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>mapping</span></a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> </p><p>(via Heng Li on twitter)</p>
Pierre Lindenbaum<p>truvari v5.0.0 released <a href="https://github.com/ACEnglish/truvari/releases/tag/v5.0.0" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/ACEnglish/truvari/r</span><span class="invisible">eleases/tag/v5.0.0</span></a> <a href="https://genomic.social/tags/sv" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sv</span></a> <a href="https://genomic.social/tags/structuralvariant" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>structuralvariant</span></a></p>
Pierre Lindenbaum<p>The PR for samtools (visualize CNVs in the <a href="https://genomic.social/tags/terminal" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>terminal</span></a> ) was merged today ! <a href="https://genomic.social/tags/samtools" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>samtools</span></a> <a href="https://genomic.social/tags/cnv" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cnv</span></a> <a href="https://genomic.social/tags/sv" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sv</span></a> <a href="https://genomic.social/tags/structuralvariant" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>structuralvariant</span></a> <a href="https://genomic.social/tags/ascii" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ascii</span></a> <a href="https://github.com/samtools/samtools/pull/1910" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/samtools/samtools/p</span><span class="invisible">ull/1910</span></a></p>
Pierre Lindenbaum<p>The future release of <a href="https://genomic.social/tags/delly2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>delly2</span></a> will contain a 'Pan-genome based SV caller' <a href="https://github.com/dellytools/delly/commit/00bdb661f6524623a4da275c0beb4331d8f7d4a3#diff-7e4c9a6f514d8ac9f231bdc1ce58ddae1fa9bdbfb05f7055fc401d71d2039ee0R46" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/dellytools/delly/co</span><span class="invisible">mmit/00bdb661f6524623a4da275c0beb4331d8f7d4a3#diff-7e4c9a6f514d8ac9f231bdc1ce58ddae1fa9bdbfb05f7055fc401d71d2039ee0R46</span></a> <a href="https://genomic.social/tags/sv" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sv</span></a> <a href="https://genomic.social/tags/structuralvariant" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>structuralvariant</span></a> <a href="https://genomic.social/tags/pangenome" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>pangenome</span></a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a></p>
Pierre Lindenbaum<p><a href="https://github.com/PopicLab/cue" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">github.com/PopicLab/cue</span><span class="invisible"></span></a> Cue: a deep learning framework for SV calling and genotyping <a href="https://genomic.social/tags/structuralVariant" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>structuralVariant</span></a> <a href="https://genomic.social/tags/sv" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sv</span></a> </p><p><a href="https://www.nature.com/articles/s41592-023-01799-x" rel="nofollow noopener" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">nature.com/articles/s41592-023</span><span class="invisible">-01799-x</span></a></p>
Pierre Lindenbaum<p>"Structural variation across 138,134 samples in the TOPMed consortium" </p><p><a href="https://www.biorxiv.org/content/10.1101/2023.01.25.525428v1" rel="nofollow noopener" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">23.01.25.525428v1</span></a> </p><p><a href="https://genomic.social/tags/cnv" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cnv</span></a> <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>genomics</span></a> <a href="https://genomic.social/tags/structuralVariant" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>structuralVariant</span></a> <a href="https://genomic.social/tags/genetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>genetics</span></a></p>
Pierre Lindenbaum<p><a href="https://genomic.social/tags/cnv" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cnv</span></a> <a href="https://genomic.social/tags/structuralVariant" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>structuralVariant</span></a> <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>genomics</span></a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> A large DUP (~1Mb) quickly found using <a href="https://github.com/brentp/goleft" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">github.com/brentp/goleft</span><span class="invisible"></span></a> and confirmed by looking at the BAM files.</p>
Pierre Lindenbaum<p>what is the use of the "Pan-Genome k-mer set" in etching ? <a href="http://big.hanyang.ac.kr/ETCHING/document.html" rel="nofollow noopener" target="_blank"><span class="invisible">http://</span><span class="ellipsis">big.hanyang.ac.kr/ETCHING/docu</span><span class="invisible">ment.html</span></a> <a href="https://genomic.social/tags/SV" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SV</span></a> <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>genomics</span></a> <a href="https://genomic.social/tags/structuralVariant" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>structuralVariant</span></a> <a href="https://genomic.social/tags/genetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>genetics</span></a></p>
Pierre Lindenbaum<p>Inversion of the day .<br><a href="https://genomic.social/tags/IGV" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>IGV</span></a> <a href="https://genomic.social/tags/inversion" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>inversion</span></a> <a href="https://genomic.social/tags/SV" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SV</span></a> <a href="https://genomic.social/tags/structuralVariant" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>structuralVariant</span></a></p>
Pierre Lindenbaum<p>"It's sunday <a href="https://genomic.social/tags/CNV" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>CNV</span></a> !" 🍾 </p><p> <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>genomics</span></a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://genomic.social/tags/structuralVariant" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>structuralVariant</span></a> <a href="https://genomic.social/tags/sv" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sv</span></a> <a href="https://genomic.social/tags/cnv" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cnv</span></a> </p><p>(made with <a href="https://lindenb.github.io/jvarkit/SwingBamCov.html" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">lindenb.github.io/jvarkit/Swin</span><span class="invisible">gBamCov.html</span></a> )</p>
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