User: mab658
mab658 • 20
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- 2 months, 2 weeks ago
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- 3 months, 4 weeks ago
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Posts by mab658
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... Hi Pierre,
I wanted to merge VCF files which had already splitted by chromosones into a single file. Though each is compressed i.e. chr1.vcf.gz, chr2.vcf.gz, ......chrn.vcf.gz.
I could not see any an output file merged.vcf.gz when I used the command. Is it because the file is compressed?
java ...
written 10 weeks ago by
mab658 • 20
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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 3 months ago by
mab658 • 20
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... I am using beagle 5.0 program for imputation. ...
written 3 months 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 3 months 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 3 months ago by
mab658 • 20
• updated
3 months ago by
Jean-Karim Heriche ♦ 18k
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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 3 months 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 3 months ago by
mab658 • 20
• updated
3 months 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 3 months 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 3 months ago by
mab658 • 20
0
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392
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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 3 months ago by
mab658 • 20
• updated
3 months ago by
Kevin Blighe ♦ 41k
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