User: otwtgin2010

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otwtgin201070
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Posts by otwtgin2010

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Comment: C: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
... Thanks and true! i guess i have a tendency to create my roof before my foundation, and the assumption that most others are the same way is an invalid one. And i don't mean this to be my personal beef about documentation that is not sufficient enough to make up for my lack of basic knowledge. Just ...
written 27 days ago by otwtgin201070
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Comment: C: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
... Thanks. Yeah, for someone who knows as much as they should, that would no doubt be plenty. But i guess for those who knows as little as i do :) - the things like how you download the file, how you extract it (or even that you need to extract it), that you need "make" installed are not self-evident ...
written 27 days ago by otwtgin201070
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Comment: C: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
... Got it - thank-you for the clarification! i tried apt-get but it was installing old versions. And the old versions were super buggy and didn't work with a lot of my sample files. ...
written 27 days ago by otwtgin201070
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Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
... Just thought I would contribute this since figuring it all out was a super confusing process consisting of a few hundred google searches. It's likely it was just me, but maybe there are a few other people like me who will benefit from being able to avoid the process. This was a clean Ubuntu 18.04 ...
samtools tutorial bcftools htslib written 27 days ago by otwtgin201070
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Comment: C: Find Intersections Between ClinVar Track and VCF In IGV
... i can confirm that after upgrading to the latest bcftools version, this works. Thanks! ...
written 4 weeks ago by otwtgin201070
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Comment: C: Find Intersections Between ClinVar Track and VCF In IGV
... Thanks. Yes, tried that also. No difference. What i did find is that i can filter with the first column of the INFO - which in this case is ALLELEID. i also saw that my bcftools version was 1.2 (this is what apt-get install pulled) - and i think the latest is 1.8. i will try and install 1.8 an ...
written 4 weeks ago by otwtgin201070
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Comment: C: Find Intersections Between ClinVar Track and VCF In IGV
... Very strange. No change at all for me. It reads the file - the filters just do not work. i had to gunzip and then bgzip separate, or else i was seeing an empty bgzip.vcf.gz file. Other than that, followed those steps exactly. gunzip clinvar_20180701.vcf.gz bgzip clinvar_20180701.vcf tabix -p ...
written 4 weeks ago by otwtgin201070
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Comment: C: Find Intersections Between ClinVar Track and VCF In IGV
... Thanks! Sorry for the delay. Very new to all this. OK - so i am banging my head against this one. Nearly as i can tell, this should work. bcftools view -i 'INFO/CLNSIG ~ "Pathogenic"' grch37_clinvar.vcf.gz i see CLNSIG in the INFO column, many of which have a value of Pathogenic, but it jus ...
written 5 weeks ago by otwtgin201070
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Find Intersections Between ClinVar Track and VCF In IGV
... Looking for a way to find the locations where a VCF and a Clinvar Track Both Have Entries. And also being able to filter these entries based on the nature of either entry. Perhaps something like finding where the VCF has a SNP/Indel at the same location the ClinVar file has an entry whose signific ...
vcf clinvar igv written 6 weeks ago by otwtgin201070 • updated 6 weeks ago by rbagnall1.3k

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