Moderator: Jeremy Leipzig
Jeremy Leipzig ♦ 19k
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- Philadelphia, PA
- Website:
- http://jermdemo.blogsp...
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I am a bioinformatics software developer known mostly for my posts on big-ass servers, damn microarray papers, and the reproducible research guilt trip, as well as my review of pipeline frameworks. I have worked in virology, crop genomics, and on various pediatric diseases as a programmer, analyst, and architect. I'm currently a PhD student at Drexel.
Posts by Jeremy Leipzig
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... saw this post mentioned in a DNANexus tutorial https://www.youtube.com/watch?v=1TcvCrszprk ...
written 3 days ago by
Jeremy Leipzig ♦ 19k
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... I find this just as succinct and less easily misinterpreted: The p-value is the probability that random chance could produce the observed difference ...
written 9 days ago by
Jeremy Leipzig ♦ 19k
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Comment:
C: GWAS summary statistics
... please post a new Biostars question ...
written 9 days ago by
Jeremy Leipzig ♦ 19k
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... I'm not sure what different models are being used to generate different lists of DE genes, but every time you do that you'd have to correct for multiple testing, even at the enrichment stage ...
written 27 days ago by
Jeremy Leipzig ♦ 19k
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... thanks for uploading this. I must say I am stumped. It does look like the overhang alignments are stopping at a particular base pair position as though there is an N in the reference that is causing a soft clip. ...
written 6 weeks ago by
Jeremy Leipzig ♦ 19k
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... can you provide an IGV screenshot of this? ...
written 6 weeks ago by
Jeremy Leipzig ♦ 19k
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... well if the duplicates are based on PCR then I'm not sure why you would say using amplicons would negate that. At any rate for variant calling I doubt removing duplicates would make a huge difference unless a sizeable proportion of duplicates were of such low quality they were leading to a variant n ...
written 6 weeks ago by
Jeremy Leipzig ♦ 19k
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... a gVCF can only handle one individual, so you couldn't use them call trios with tools that expect a trio VCF
(correction: yes there are multi-sample gVCFs that briefly arise from CombineGVCFs but they are never found in the wild) ...
written 6 weeks ago by
Jeremy Leipzig ♦ 19k
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... You'll need a VCF with the trio(s), not 45 gVCFs, so GenotypeGVCFs those together (or at least into 15 trio vcfs)
Annotate with [snpEff][1]
java -Xmx4G -jar snpEff.jar -i vcf -o vcf GRCh37.69 trio.vcf > trio_snpeff.vcf
and then to get variant frequencies, annotate with gnomAD using VCFanno ...
written 7 weeks ago by
Jeremy Leipzig ♦ 19k
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... Yes AF is the MAF here.
It bears mentioning that sometimes the variant might not necessarily be the less common allele in all populations, and the major allele might even confer something weakly deleterious. But in these two cases, they only saw one individual with this mutation. ...
written 8 weeks ago by
Jeremy Leipzig ♦ 19k
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