User: Ana

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Ana0
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Posts by Ana

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extract DP of heterozygotes from vcf file
... Hi everyone I want to plot the read distribution only in heterozygote genotypes in my vcf file. Does anyone has any idea how to extract only DP values of heterozygotes? Thanks ...
heterozygotes vcffile sample read depth written 4 days ago by Ana0 • updated 4 days ago by Pierre Lindenbaum92k
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difference between read depth (DP) at site (INFO) and sample(FORMAT) level
... I am a bit confused between read deapth at the site level and sample level. What is the difference between these two? This is a little part of my vcf file, So I have DP at INFO and FORMAT ! This is my Site annotation AN=662;AO=323;CIGAR=1X;DP=225 and this is my sample level annotation GT ...
read depth vcf file written 19 days ago by Ana0
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how to filter vcf file based on sample DP? vcf tools does not work
... I have faced with a problem in filtering my vcf file, I am quite stuck. I have tried several options but none of them worked out. I want to do filtering at the "sample level" and keep only those with DP >=10. I have tried in VCFtools --minDP flag and --maxDP are not working! I have tried all o ...
vcf-filtering sample dp written 20 days ago by Ana0
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Comment: A: extract sample DP values from VCF
... Alright, this is my code /data/programs/vcftools_0.1.13/bin/vcftools --vcf my_file.vcf --geno-depth --recode --out results1.vcf bu I get an error message: Error: Only one output function may be called. any suggestion for this problem? ...
written 21 days ago by Ana0
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extract sample DP values from VCF
... I want to extract only sample DP values (the second value in the example below) from my cvf file, this is my genotype annotation 0/0:7:7,0:7:244:0:0:0,-2.10721,-20.8228 0/1:3:3,1:2:74:1:37:-2.76372,0,-3.15643 0/0:9:9,0:9:321:0:0:0,-2.70927,-19.2273 0/0:11:11,0:11:407:0:0:0,-3.31133 ...
vcf perl vcf tools vcf filtering written 24 days ago by Ana0 • updated 19 days ago by noeD50
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Comment: C: calculating genotype quality from genotype likelihood
... I actually did find some ideas from the post by Philip https://www.biostars.org/p/104824/ They suggested to calculate genotype likelihood ratio. Does any one have any idea about good threshold value for this? ...
written 5 weeks ago by Ana0
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calculating genotype quality from genotype likelihood
... Hi all, I have faced with a question and I would appreciate if anyone has any comment or suggestion. I have got a vcf file made by FreeBayes, genotype quality is missing. I want to filter out those below the cutoff value. Therefore I want to know how can I get (calculate) genotype quality from geno ...
genotype likelihood genotype quality freebayes written 5 weeks ago by Ana0 • updated 5 weeks ago by youcai10
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Comment: C: creating for loops in R for nGS data
... actually someone gave me the solution: Works perfectly fine data$keep_dontKeep <- "dontKeep" for (i in 1:nrow(data)){ if(as.character(data$V1[i]) == as.character(data$V4[i])){ #If values in V1 and V3 are equal, categorize as 'keep' data$keep_dontKeep[i] <- "keep" } } data < ...
written 11 weeks ago by Ana0
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creating for loops in R for nGS data
... I have a question about doing a for loop in R, I would be very grateful if you could let me know your ideas. I'm working with NGS data, I have calculated r2 values to estimate linkage disequilibrium but I want to calculate LD decay for every single SNP in each contig. This is the first 3 rows of my ...
loops R written 11 weeks ago by Ana0 • updated 11 weeks ago by TriS2.6k

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