User: AVA
AVA • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- Finland
- Last seen:
- 2 days, 5 hours ago
- Joined:
- 2 weeks, 6 days ago
- Email:
- v************@helsinki.fi
Posts by AVA
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... I am new to the field of genomics. I would like to perform a PCA using 1K data. My data is in 38 build and therefore, I would like to download 1K phase 3 data in 38 build from the site below:
http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/
I have no clue how ...
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... I am trying to change genomic coordinates for 1kHG data from hg37 to hg38 using CrossMap. I have Crossmap.py in the folder CrossMap at path /fs/projects/..../CrossMap/bin/CrossMap.py. I have never run a python script before. I understood that I am supposed to set python3 path to run this script. I u ...
written 2 days ago by
AVA • 10
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... Thank you for your time and suggestions. I used bcftools view (/bcftools view output.vcf > output_vcf.vcf) convert the binary format to vcf format and rvtest accepts this file. ...
written 10 days ago by
AVA • 10
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... Sorry, I misunderstood you. I am quite new to working in genomics. Using bcftools view -h output.vcf, the header of a an output file for e.g. for chr10 appears as below. I am working on single chromosome imputed data.
##fileformat=VCFv4.2
##FILTER=
##filedate=20190717
##source="beagle.27Jan18.7e1. ...
written 11 days ago by
AVA • 10
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... Thank you for your assistance. I have edited the original question ...
written 12 days ago by
AVA • 10
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... Using bcftools view -h output.vcf, the header has IDs of the participants as: number_string ...
written 12 days ago by
AVA • 10
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... Do you mean in this command?
/bcftools +prune -m 0.15 -w 1000 input.vcf -Ob -o output.vcf
Can you please elaborate?
...
written 12 days ago by
AVA • 10
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... When I open the file,I get a warning: may be a binary file. See it anyway?
When I use an extension vcf.gz in the output file while pruning. The file header looks like below:
BCF^B^B^A^A^@##fileformat=VCFv4.2
A lot of meta-data in between followed by the usual vcf header CHROM POS etc followed by ...
written 12 days ago by
AVA • 10
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... I want to calculate kinship matrix for autosomes in order to run a LMM. For this purpose, I first pruned each autosome using bcftools (version 1.11) and excluded the snps that had r2 greater than 0.15 by utilizing the command:
/bcftools +prune -m 0.15 -w 1000 input.vcf -Ob -o output.vcf
When I use ...
written 12 days ago by
AVA • 10
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... Thank you. I have bcftools-1.11 and yes the above command did work but with -m instead of -l. ...
written 17 days ago by
AVA • 10
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