User: AVA

gravatar for AVA
AVA10
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

<prev • 11 results • page 1 of 2 • next >
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Downloading 1000genome phase 3 data in 38 build
... 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 ...
1khg build38 download written 2 days ago by AVA10 • updated 2 days ago by ATpoint46k
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Converting 1kHG genomic coordinates from hg37 to hg38 build
... 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 ...
hg37 to hg38 python3 crossmap 1khg written 2 days ago by AVA10
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Comment: C: The pruned in file by bcftools gives error "Wrong VCF header" while calculating
... 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 AVA10
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Comment: C: The pruned in file by bcftools gives error "Wrong VCF header" while calculating
... 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 AVA10
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Comment: C: The pruned in file by bcftools gives error "Wrong VCF header" while calculating
... Thank you for your assistance. I have edited the original question ...
written 12 days ago by AVA10
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Comment: C: The pruned in file by bcftools gives error "Wrong VCF header" while calculating
... Using bcftools view -h output.vcf, the header has IDs of the participants as: number_string ...
written 12 days ago by AVA10
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Comment: C: The pruned in file by bcftools gives error "Wrong VCF header" while calculating
... 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 AVA10
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Comment: C: The pruned in file by bcftools gives error "Wrong VCF header" while calculating
... 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 AVA10
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The pruned in file by bcftools gives error "Wrong VCF header" while calculating kinship matrix using Rvtests
... 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 ...
software error written 12 days ago by AVA10
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Comment: C: Pruning a VCF file and extracting pruned in snps using bcftools
... 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 AVA10

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