User: Ana

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Ana0
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Posts by Ana

<prev • 14 results • page 1 of 2 • next >
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Comment: C: how to extract a random set of SNP from a SNP table
... Many many thanks WouterDeCoster, it works perfectly :) ...
written 13 days ago by Ana0
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Comment: C: how to extract a random set of SNP from a SNP table
... thanks a lot WouterDeCoster, sorry I was away and just checked the code now. It seems that it does not work, I do not have the experience of Python. I get this error message > Traceback (most recent call last): File "./Lineselector.py", line 7, > in > for line in open(sys.argv[1]): ...
written 13 days ago by Ana0
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Comment: C: how to extract a random set of SNP from a SNP table
... Thanks for your comment but I do not get it well, could you please explain a bit more?I appreciate that I have more than 11 million lines! the probability that a particular line will get included is equal to other lines. ...
written 25 days ago by Ana0
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Comment: C: how to extract a random set of SNP from a SNP table
... I need approximately 10K ...
written 25 days ago by Ana0
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how to extract a random set of SNP from a SNP table
... I have a SNP table (tab.table format) ,containing more than 10000K SNPs (its a whole genome data). Now I need to extract a random set of 10k SNPs chosen approximately equally spaced along the chromosomes (17 chromosomes). Could you please help me to figure out how to do that? thanks in advance for a ...
extraction random sample snp written 26 days ago by Ana0 • updated 13 days ago by Alex Reynolds19k
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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 5 weeks ago by Ana0 • updated 5 weeks ago by Pierre Lindenbaum94k
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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 7 weeks 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 7 weeks 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 7 weeks 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 8 weeks ago by Ana0 • updated 7 weeks ago by noeD50

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