User: mab658

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mab65820
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Posts by mab658

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Calculate mean_GQ value from individual GQ values in a multi-sample VCF file
... 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 mab65820
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Comment: C: how to generate genetic maps from VCF snps data
... I am using beagle 5.0 program for imputation. ...
written 13 days ago by mab65820
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how to generate genetic maps from VCF snps data
... 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 ...
snp sequencing written 13 days ago by mab65820
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why filtering sites with allele count below 3
... 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 ...
snp sequencing written 16 days ago by mab65820 • updated 15 days ago by Jean-Karim Heriche17k
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Comment: C: How to filter vcf file on minimum genotype depth and quality for each sample
... 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 mab65820
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Conversion of imputed VCF file to HapMap format
... Hi Everyone, I have successfully imputed my VCF file using beagle4.1. How do I convert it to HapMap format, please? Thanks. ...
rna-seq snp written 19 days ago by mab65820 • updated 18 days ago by 159932162500
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Comment: C: Filtering of low coverage variants from VCF
... 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 mab65820
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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 mab65820
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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 mab65820 • updated 20 days ago by Kevin Blighe35k
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Conversion of imputed output file from beagle 4.1 to vcf dosage format
... 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 ...
rna-seq snp sequencing written 21 days ago by mab65820 • updated 21 days ago by RamRS20k

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