User: Arko
Arko • 10
- 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
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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
Arko • 10
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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
Arko • 10
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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
Arko • 10
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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
Arko • 10
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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
Arko • 10
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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
Arko • 10
10
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... 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 ...
written 3 months ago by
Arko • 10
• updated
12 weeks ago by
Emily_Ensembl ♦ 16k
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... 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 ...
written 3 months ago by
Arko • 10
• updated
3 months ago by
Emily_Ensembl ♦ 16k
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... 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
Arko • 10
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... 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
Arko • 10
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