User: jan

gravatar for jan
jan60
Reputation:
60
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Trusted
Location:
Malaysia
Last seen:
3 days, 10 hours ago
Joined:
2 years, 8 months ago
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Posts by jan

<prev • 30 results • page 1 of 3 • next >
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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 days ago by jan60
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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 9 days ago by jan60 • updated 8 days ago by prasundutta87150
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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 6 months ago by jan60
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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 6 months ago by jan60 • updated 6 months ago by Vivek1.9k
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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 10 months ago by jan60
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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 12 months ago by jan60 • updated 12 months ago by Shicheng Guo4.5k
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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 14 months ago by jan60
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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 14 months ago by jan60 • updated 14 months ago by Chris Cole640
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Comment: C: Interpretation of TCGA clinical data
... Hi, Can I just ask how did you parse the XML files ? ...
written 16 months ago by jan60
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Comment: C: annotating TCGA VCF file
... Thank you for your reply. I just submitted a contact form through The McDonnell Genome Institute Websitey website . It's quite difficult to navigate the new TCGA portal and there is no option to get MAF files for whole exome sequencing data. There are only BAM and VCF files. I found a website in ...
written 16 months ago by jan60

Latest awards to jan

Popular Question 6 months ago, created a question with more than 1,000 views. For Extract each annotation in 'info' column in snpEff output
Popular Question 6 months ago, created a question with more than 1,000 views. For Predicting functional effects of a mutation
Popular Question 6 months ago, created a question with more than 1,000 views. For problem to download 1000genome database using ANNOVAR
Popular Question 6 months ago, created a question with more than 1,000 views. For Question : Annotating dbNSFP using snpSIFT , problem with index
Popular Question 10 months ago, created a question with more than 1,000 views. For Predicting functional effects of a mutation

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