User: Arko

gravatar for Arko
Arko10
Reputation:
10
Status:
New User
Location:
US/Boston/Boston University
Last seen:
2 months, 4 weeks ago
Joined:
9 months, 2 weeks ago
Email:
a*****@bu.edu

Posts by Arko

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Querying VEP using REST API
... All fields into a tsv or a csv format preferably. Something that's easy to read. Right now it's a mess when outputting into a text file directly. ...
written 12 weeks ago by Arko10
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Comment: C: Querying VEP using REST API
... That makes a lot of sense, it has 5000 variants. Chunk it into separate queries? Sounds time consuming to run 25+ chunks. Would you have a quicker or a more efficient way of going about this? ...
written 12 weeks ago by Arko10
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Comment: C: Querying VEP using REST API
... Doesn't seem to work for me, receiving a HTTP 400 error. I've tried using a list as well as just a string with each rsid in a new line. ...
written 12 weeks ago by Arko10
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Comment: C: VEP JSON output parsing
... On the off-chance, I too am working on a parser. I was wondering if you could link me to yours and that may probably help me out? Thanks in advance! ...
written 12 weeks ago by Arko10
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Comment: C: Querying VEP using REST API
... One question, do you have a good way of parsing or formatting the JSON output ? Right now I'm outputting everything into a text file. ...
written 12 weeks ago by Arko10
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Comment: C: Querying VEP using REST API
... rs2329763 rs6716521 rs4686605 rs9290916 rs7622109 rs16877127 rs160885 rs16908004 rs622120 rs970275 . . 1000 rows more ...
written 3 months ago by Arko10
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Querying VEP using REST API
... I'd like to query a JSON output for VEP using the REST API. I have the following code in python 3, can anyone tell me where I'm going wrong? I'm getting a HTTP 400 error. import json import requests import sys enter code here`with open('sample.tsv','r') as file: for line in fil ...
rest ensembl vep python R written 3 months ago by Arko10 • updated 12 weeks ago by Emily_Ensembl16k
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Querying variations from a VCF file
... I have a VCF file v4.1 and I'm trying to extract the type of variations (Substitution, Insertion, Silent, Intergenic, etc.) from it. If there are multiple possibilities, how would I annotate the most deleterious possibility? Apart from that, I'm trying to find the number of reads supporting the var ...
vcf bioinformatics variants mutations python written 3 months ago by Arko10 • updated 3 months ago by Emily_Ensembl16k
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Comment: C: Merging and converting multiple vcf files into a SNP array
... Tried it, but BCF tools on merge considers the NON - REF as a literal allele call instead of ignoring it and a NON-REF contributes to the genotype call. ...
written 6 months ago by Arko10
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Comment: C: Merging and converting multiple vcf files into a SNP array
... GATK doesn't allow merging of VCF and gVCF files unfortunately. My aim is to obtain a single VCF file from the entire set, ...
written 6 months ago by Arko10

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