User: mab658
mab658 • 20
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Posts by mab658
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... This is what I have been looking for. I applied it to my work and it went well. I have chrom, pos, and sample with their respective GQ values. How do I get the average across all the samples for each site (i.e chrom and pos). I need the average so that I can plot it in R. ...
written 10 days ago by
mab658 • 20
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... I am using beagle 5.0 program for imputation. ...
written 13 days ago by
mab658 • 20
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... Hi Everyone,
Could someone guide me on how to generate genetic map from snps VCF file in order to use it for imputation. I have filtered my snps VCF file and I need genetic map for the imputation. I got to know that one can use PLINK. I need to know what I need to extract from my data prior to us ...
written 13 days ago by
mab658 • 20
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... Hi everyone,
I came across SNP filtering tutorial where the author used the flag `--mac 3` to filter SNPs that have a minor allele count less than 3. That is `vcftools --vcf input_file.vcf --mac 3 --recode --out filtered_file`
Could someone explain to me why filtering out sites with minor allele ...
written 16 days ago by
mab658 • 20
• updated
15 days ago by
Jean-Karim Heriche ♦ 17k
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... from the above script, --minGQ and --minDP take the value of 15 and 10 respectively for filtering genotype quality and depth. Is there any criteria for choosing 15 and 10.. Just to know if 15 and 10 are standard values to use for those flags. ...
written 18 days ago by
mab658 • 20
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... Hi Everyone,
I have successfully imputed my VCF file using beagle4.1. How do I convert it to HapMap format, please?
Thanks. ...
written 19 days ago by
mab658 • 20
• updated
18 days ago by
15993216250 • 0
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... Dear All,
I am having similar problem in determining the appropriate filtering criteria for the snps depth and quality. I am just a beginner in using `vcftools` for snps call filtering.How do i translate the hard filters below using vcftools: that is
QualByDepth (QD) 2.0
FisherStrand (FS) 60.0
RMSMa ...
written 19 days ago by
mab658 • 20
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Comment:
C: Imputation of vcf file
... Thanks Kevin. Your response has been very helpful! Prior to imputation, I cleaned my VCF file using
`vcftools` --gzvcf snps.vcf.gz --maf 0.01 --max-missing 0.8 --min-meanDP 10 --recode --out snp_filtered.vcf.gz
Please how do I filter 'junk' variants that have a high statistical probability of bein ...
written 20 days ago by
mab658 • 20
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Comment:
C: Imputation of vcf file
... After imputation using beagle 4.1, I have output with genotypes phased like 0|0, 0|1, etc as follows:
##fileformat=VCFv4.2
##filedate=20181226
##source="beagle.27Jul16.86a.jar (version 4.1)"
##INFO=
##INFO=
##INFO=
##INFO=
##FORMAT=
##FORMAT=
##FORMAT=
#C ...
written 20 days ago by
mab658 • 20
• updated
20 days ago by
Kevin Blighe ♦ 35k
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... A filtered VCF file has been successful imputed using beagle 4.1 as follows:
java -Xmx24g -jar /programs/beagle41/beagle41.jar gt=/workdir/moshood/snps/snp_filtered.vcf.gz.recode.vcf nthreads=8 niterations=0 out=imputed_file
The output file named impute_file is phased and imputed. Could anyon ...
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