User: jan
jan • 140
- Reputation:
- 140
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- Location:
- Sydney, Australia
- Last seen:
- 2 months, 1 week ago
- Joined:
- 5 years, 11 months ago
- Email:
- j**********@gmail.com
Posts by jan
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... Hi, Im having the same issue. Have you found a solution to search for those motif based on VEP motif (ENSM..........). ? ...
written 10 weeks ago by
jan • 140
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... Thanks for the correction Ben. It is now working as intended. ...
written 3 months ago by
jan • 140
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... Thanks Ben. I dont think --gz flag was the issued. I still can get the ouput without the --gz flag. But variants in my outputs dont passed all of the filters
When I combined all my filters in one line such as below without the --gz flag, i get my desired output. ie variants passing all my filters. ...
written 3 months ago by
jan • 140
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... Hi,
I'm trying to filter my VCFs using filter_vep ([https://asia.ensembl.org/info/docs/tools/vep/script/vep_filter.html][1]) following certain criteria. Variants in my output need to pass all filters.
filter_vep \
--input_file input.vcf.gz \
--output_file out.vcf \
...
written 3 months ago by
jan • 140
• updated
3 months ago by
Ben_Ensembl • 1.6k
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... Hi,
I'm trying to view structural variants (>50bp) from PacBio long read sequencing on IGV. I have been unable to hide the small indels (likely errors) using these settings:
∗ Alignment Track Options: Hide indels < 10 bases
∗ Coverage Track Options: Coverage allele-fraction threshold: 0.25
∗ ...
written 15 months ago by
jan • 140
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Comment:
C: Automatic IGV snapshot script
... Hi Steve,
I'm trying to use your tool to view bam files located on a remote server. I'm getting an error when I tried running the demo. See below. Could you please advice how to fix or troubleshoot this error. Thank you.
Read 4 regions
xdpyinfo: unable to open display ":1".
Open Xvfb port found ...
written 15 months ago by
jan • 140
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Comment:
C: Annotation for SV and CNV
... Is this tool suitable for SVs sequenced from PacBio long reads and called using Sniffle? ...
written 16 months ago by
jan • 140
5
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... Hi All,
I'm pretty new in analysing SV and CNV. We have WGS PacBio long reads germline sequencing reads that have been aligned using pbalign tool to reference sequences （GRCh37/hg19). Variants were called using the variantCaller.py from GenomicConsensus package (https://github.com/PacificBioscienc ...
written 16 months ago by
jan • 140
• updated
16 months ago by
WouterDeCoster ♦ 45k
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... Hi,
I want to include number of papers cited a certain journal (can be obtained from google scholar) and the journal current impact factor to my references.
Is there a tool to export such information from google scholar to endnote? or Excel, or any relevant working sheet. I have 300+ citations t ...
written 2.3 years ago by
jan • 140
0
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... 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 2.7 years ago by
jan • 140
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