User: Lauren

gravatar for Lauren
Lauren50
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1 year ago
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2 years, 5 months ago
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m*******@mit.edu

Posts by Lauren

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Comment: C: CNVkit: gene results not in output
... Thanks so much for getting back, Eric! -I ran it with really basic options, see below: cnvkit.py coverage $bamFile $target -o $outTgtCnn cnvkit.py coverage $bamFile $antitarget -o $outATgtCnn cnvkit.py fix $outTgtCnn $outATgtCnn $reference -o $outRatioCnr cnvkit.py segment $outRati ...
written 13 months ago by Lauren50
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CNVkit: gene results not in output
... I am looking at a few illumina WES experiments on the same cell line, trying to find a cnkit segment or bin hit on a gene that has reads and is captured in the library. I am not finding any values in all but one sample (no neutral calls, just omitted). The location is represented in the target file. ...
cnvkit written 14 months ago by Lauren50 • updated 13 months ago by Eric T.2.5k
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Answer: A: How to find the mapping quality (mapQ) score of a variant
... You could get the mapping qualities at the positions of the variants using mpileup on the SAM and take the mean/median. Check the XA and XT tags if you generated them to see whether the position had alternate mappings and how close to your reads they were. ...
written 2.1 years ago by Lauren50
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Is SNPeff still the standard for variant effect prediction?
... I'm kind of new to this space-- a friend of mine says he uses SNPeff for all his exome annotations, and he doesn't know of any other popular tools for this purpose. I'm annotating some human exomes and I am curious about what else is out there. A search gave me a lot of answers, but I don't know w ...
exome annotation snpeff variant written 2.1 years ago by Lauren50 • updated 11 weeks ago by Shicheng Guo7.7k
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Comment: C: CNVkit Segments vs Bins
... Thank you very much. ...
written 2.2 years ago by Lauren50
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Comment: C: CNVkit Segments vs Bins
... Thank you very much. ...
written 2.2 years ago by Lauren50
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Variant callers reporting different read depth on same alignment
... I generated two VCFs, one with freebayes and one with GATK on the same BAM file. At one position, freebayes called an MNV. At the same position, GATK called an SNV. What confuses me is that the depths are different in the VCF file. for example, freebayes called: chr 9 35906602 C A,T 0/1 6,7,6:1 ...
variant calling gatk freebayes variant annotation written 2.3 years ago by Lauren50 • updated 2.3 years ago by Pierre Lindenbaum122k
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CNVkit Segments vs Bins
... After reading the paper and docs, I am having a little trouble understanding the difference and usage for calling at the segment level or the bin level. I am running CNVkit using human exome seq data. My questions are: What use case would the segment level calls be best for What use case would th ...
exome cnvkit copy number segment written 2.5 years ago by Lauren50 • updated 2.5 years ago by Eric T.2.5k

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Supporter 2.1 years ago, voted at least 25 times.

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