User: Lauren

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Lauren70
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Posts by Lauren

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Answer: A: refsnp API has different positions for SNPs in same reference
... edit: I think this answers my question -- I'll leave it up in case someone has the same question later on: https://ncbiinsights.ncbi.nlm.nih.gov/2017/02/09/new-web-services-for-comparing-and-grouping-sequence-variants ...
written 14 days ago by Lauren70
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refsnp API has different positions for SNPs in same reference
... For example here's a specific rsid: https://www.ncbi.nlm.nih.gov/snp/rs62123481 On the ncbi SNP website, the position in GRCh38.p12 is reported as 38384432. In the hgvs, it also has 38384432. Same in the VCF. But in the chr19 json file I downloaded from refsnp, it gives 38384431 as the position. I ...
refsnp json dbsnp rsid api written 14 days ago by Lauren70
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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 24 months ago by Lauren70
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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 2.0 years ago by Lauren70 • updated 2.0 years ago by Eric T.2.6k
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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 3.0 years ago by Lauren70
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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 3.0 years ago by Lauren70 • updated 13 months ago by Shicheng Guo8.3k
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Comment: C: CNVkit Segments vs Bins
... Thank you very much. ...
written 3.1 years ago by Lauren70
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Comment: C: CNVkit Segments vs Bins
... Thank you very much. ...
written 3.1 years ago by Lauren70
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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 3.2 years ago by Lauren70 • updated 3.2 years ago by Pierre Lindenbaum129k
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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 3.3 years ago by Lauren70 • updated 3.3 years ago by Eric T.2.6k

Latest awards to Lauren

Popular Question 23 months ago, created a question with more than 1,000 views. For CNVkit Segments vs Bins
Popular Question 23 months ago, created a question with more than 1,000 views. For Is SNPeff still the standard for variant effect prediction?
Popular Question 23 months ago, created a question with more than 1,000 views. For Variant callers reporting different read depth on same alignment
Student 23 months ago, asked a question with at least 3 up-votes. For Is SNPeff still the standard for variant effect prediction?
Supporter 3.0 years ago, voted at least 25 times.

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