User: nikitavlassenko

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Posts by nikitavlassenko

<prev • 35 results • page 1 of 4 • next >
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Comment: C: Where to get GERP_scores.final.sorted.txt.gz for VEP analysis
... The download is not working. If you go to the next step you will see that it is not going to be downloaded OR there are some weird Firewall rules on my job. I have not yet tried doing it outside from regular wifi. ...
written 13 days ago by nikitavlassenko40
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Where to get GERP_scores.final.sorted.txt.gz for VEP analysis
... I need to run the pipeline: https://github.com/macarthur-lab/hail-elasticsearch-pipelines/tree/master/luigi_pipeline It has a VEP annotation step and the config file used is: https://storage.googleapis.com/seqr-hail/vep/vep85-loftee-gcloud.json In this file I need to set a bunch of paths to VEP ...
vep hail gerp written 15 days ago by nikitavlassenko40 • updated 15 days ago by genomax75k
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Extract columns from VCF file using bcftools preserving all the header info
... I am trying to extract only the columns I need from VCF preserving VCF structure, its header, its formatting. I am using bcftools. I tried doing: ``` bcftools annotate -c CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO/AF,INFO/AC,INFO/AN Holland.vcf -o Holland_selected_cols.vcf ``` But the output file just ...
vcf bcftools written 25 days ago by nikitavlassenko40 • updated 25 days ago by finswimmer13k
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Answer: A: Automatic parsing of VCF and correcting value types
... What ultimately worked for just substitution of 'nan' to zeros in VCF is the following script: ``` #!/bin/bash # Remove all 'nan' of type {paramName}=nan and of type [{floatNum}, nan] sed_commands_array=("s/\([A-Z_a-z0-9]*\)=nan\([,;]\)/\1=0\2/g;" "s/\([[-]\?[0-9]*\.\?[0-9]*\), nan/\1, 0/g;" "s/\ ...
written 26 days ago by nikitavlassenko40
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Comment: C: Automatic parsing of VCF and correcting value types
... I tried making it match the other pattern but it is not working: ``` sed 's/\(\[([0-9]*[.])?[0-9]+[, ]+\)nan;/\1, 0;/g' ``` ...
written 26 days ago by nikitavlassenko40
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Comment: C: Automatic parsing of VCF and correcting value types
... Still getting an error: unable to convert [1.618, nan] (of class java.util.ArrayList) to Array[Double] Probably need to add [...] somehow I am thinking of just using ```sed 's/nan/0/g'``` but afraid that if 'nan' happens as a part of some name, it will be mistakenly substituted ...
written 26 days ago by nikitavlassenko40
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Comment: C: Automatic parsing of VCF and correcting value types
... I am wondering, what is ATT? I need to somehow check the whole file, find 'nan', then check what is the field type, and then change it to String. Another way - and maybe way simpler - would be just to substitute 'nan' to zero, but is it correct? Maybe it is, I just try to make sure that it would not ...
written 26 days ago by nikitavlassenko40
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Automatic parsing of VCF and correcting value types
... I have a pipeline written in Hail 0.1 for VCF processing: https://github.com/macarthur-lab/hail-elasticsearch-pipelines The pipeline can't process VCF files that have 'nan' values in 'Float' - type of fields. So, I found the solution of making a fake header with 'String' - types instead of 'Float' ...
vcf nan written 26 days ago by nikitavlassenko40
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Comment: C: Differential gene analysis from a javascript based web app
... I need something like this: https://docs.microsoft.com/en-us/machine-learning-server/deployr/deployr-about But I do not want to use DeployR server itself, just need such an API. ...
written 14 months ago by nikitavlassenko40
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Comment: C: Differential gene analysis from a javascript based web app
... What about server-side javascript? I have `node.js` on the server. Maybe there are any other libraries in other languages that could be accessed easily from javascript? Like `C++`, idk... I actually think that `OpenCPU` is the right way to go, I am just not sure how to call it on the server from my ...
written 14 months ago by nikitavlassenko40

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Supporter 25 days ago, voted at least 25 times.
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