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User: jan

gravatar for jan
jan • 90
Reputation:
90
Status:
Trusted
Location:
Malaysia
Last seen:
2 weeks, 4 days ago
Joined:
3 years, 4 months ago
Email:
j**********@gmail.com

Posts by jan

<prev • 31 results • page 1 of 4 • next >
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Comment: C: tools to calculate Exac population specific frequency
... I ended up following above suggestion. MAF (mutation allele format) is a format of my variant file. My sequencing vcf files were initially anonated with snpEff and in-house qSNP. So what we did was to re-annotate vcf files using VEP and use their ExAC plugin which can calculate frequency from AN, ...
written 7 weeks ago by jan • 90
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Comment: A: annotating strand orientation
... HI, My VCF has information regarding the strandbias which is not what Im asking. What I need to know is the orientation of the transcripts , either on forward or reverse direction. eg BRCA1 transcript is on the reverse transcript. I have looked in my VCF and it's missing the transcript orientation ...
written 8 months ago by jan • 90
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annotating strand orientation
... Is there a way to annotate my VCF with the transcript orientation ? Is there any reference for strand orientation ? ...
vcf sequencing written 8 months ago by jan • 90 • updated 8 months ago by prasundutta87 • 170
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Comment: C: tips for checking variants in IGV
... Thank you for your feedback. Apart from that, I would also like to know what kind of parameters should I set ? For example in View > Alignments ; there are few options such as Alignment Track Options (particularly mapping quality threshold), Coverage Track options, etc? Is it ok if I just leav ...
written 14 months ago by jan • 90
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tips for checking variants in IGV
... Hi, I need to check some germline variants on IGV from BAM files based on their positions. Is there a good tutorial/guide on how to set up parameters/filters in IGV and the reasoning behind them? Im only aware of the basic parameters such as strand-bias, variant on >20% reads. ...
bam igv germline written 14 months ago by jan • 90 • updated 14 months ago by Vivek • 2.1k
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tools to calculate Exac population specific frequency
... HI, I have 500+ MAF files of exome sequencing. I want to get the allele frequency for all population in Exac. I have used awk script to match my variants in MAF files with the VCFs from EXac database. However, Exac only provides the allele count and allele number (AC ; AN) for population specific ...
maf exac sequencing written 18 months ago by jan • 90
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TCGA MSI status
... Hi, Im trying to find the MSI-status for TCGA samples and couldn't find the information in clinical/clinical supplement and biospecimen/biospecimen supplement files. What i need looks something like this: https://wiki.nci.nih.gov/display/TCGA/Microsatellite+data Where can I find these informati ...
tcga msi clinical written 20 months ago by jan • 90 • updated 20 months ago by Shicheng Guo • 5.0k
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Comment: C: predict deleteriousness of nonsense variants
... Thank you for the information, However, most of the tools are designed to predict nonsynonymous missese based on multiple sequence alignment i.e variants at conserved site are likely to have larger functional impact. And also some other algorithms that make use protein biochemical properties, domai ...
written 22 months ago by jan • 90
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predict deleteriousness of nonsense variants
... Hi, Is there any good prediction tools that can predict deliriousness of nonsense variants? Im trying to prioritize germline variants that might be potentially pathogenic to the disease that I'm investigating. After filtering for rare variants, and my genes of interest, i still have quite a numbe ...
polyphen wgs exome sequencing sift dbnsfp written 22 months ago by jan • 90 • updated 22 months ago by Chris Cole • 660
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Comment: C: Interpretation of TCGA clinical data
... Hi, Can I just ask how did you parse the XML files ? ...
written 24 months ago by jan • 90

Latest awards to jan

Popular Question 7 months ago, created a question with more than 1,000 views. For Extract each annotation in 'info' column in snpEff output
Popular Question 7 months ago, created a question with more than 1,000 views. For filter multiple VCF files using snpSift
Popular Question 7 months ago, created a question with more than 1,000 views. For Predicting functional effects of a mutation
Popular Question 14 months ago, created a question with more than 1,000 views. For Extract each annotation in 'info' column in snpEff output
Popular Question 14 months ago, created a question with more than 1,000 views. For Predicting functional effects of a mutation
Popular Question 14 months ago, created a question with more than 1,000 views. For problem to download 1000genome database using ANNOVAR
Popular Question 14 months ago, created a question with more than 1,000 views. For Question : Annotating dbNSFP using snpSIFT , problem with index
Popular Question 18 months ago, created a question with more than 1,000 views. For Predicting functional effects of a mutation
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