Moderator: Will

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Will4.4k
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Posts by Will

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Comment: C: Uses for low-coverage human genome sequence
... Hmm, that seemed to be exome sequencing (or at least from my 60 second scan). We are getting whole genome sequence, there's no way to enrich for exomes. But maybe using this and pooling would work. ...
written 2.3 years ago by Will4.4k
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Comment: C: Uses for low-coverage human genome sequence
... That's pretty cool. We could almost do a mini case/control GWAS study ... not sure if it would work but its worth a try. ...
written 2.3 years ago by Will4.4k
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Uses for low-coverage human genome sequence
... I have a cohort of patients that we are doing HIV deep sequencing of integrated provirus and because of the technical methods we are using we also get some of host (human) genomc sequence ... I'm estimating 2 billion bp, so ~1X coverage. Its not going to be enough coverage to capture any clinically ...
genome written 2.3 years ago by Will4.4k • updated 2.3 years ago by mikhail.shugay3.2k
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Comment: C: Edge case in VCF format
... Yup, had the wrong search terms. ...
written 2.7 years ago by Will4.4k
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Edge case in VCF format
... I'm trying to create a VCF formatted file from a pairwise alignment of two genomes. Downstream I'm going to use this to calibrate some deep-sequencing data where I know the input sequence (and thus the variants). I'm just running into an odd edge-case in the VCF format. Following the specifications ...
alignment written 2.7 years ago by Will4.4k
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Database of HERV integration locations
... Does anyone know of a database of integration sites of known Human Endogenous Retroviruses (HERVs). I've come across this resources (http://herv.img.cas.cz/) which came from this paper (http://nar.oxfordjournals.org/content/32/suppl_1/D50.abstract) in 2003 but the data behind the website is missing. ...
database written 3.0 years ago by Will4.4k • updated 3.0 years ago by Jeremy Leipzig17k
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Comment: C: Specific versions of samtools and bcftools
... That solves the samtools problem. But it doesn't seem to work for the bcftools. There's a sourceforge page for vcftools (http://sourceforge.net/projects/vcftools/) and that only goes to release 972 ...
written 3.0 years ago by Will4.4k
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Specific versions of samtools and bcftools
... So, I'm trying to figure out how I installed my `samtools` and `bcftools` versions so I can replicate it across different computers using conda. I know I installed it from the "download zipfile" on the website which gives you the most recent master clone. With all of the differences between differen ...
software written 3.0 years ago by Will4.4k
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Comment: C: Extracting a trimmed output from a bam file
... Yeah, that's what I'm seeing. I figured it would be a more common request, but I guess not ... python to the rescue! ...
written 3.1 years ago by Will4.4k
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Comment: C: Extracting a trimmed output from a bam file
... Correct. I'd prefer to exclude things that are only partially inside the region ... although I can parse that out in my downstream analysis. ...
written 3.1 years ago by Will4.4k

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