User: vinayreddynannuru

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Posts by vinayreddynannuru

<prev • 13 results • page 1 of 2 • next >
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imputation accuracy in beagle
... hello all, i wanted to calculate the imputation accuracy for my data in beagle. there is an output below when i compared my unimputed vcffile with imputed file that contains only randomly selected positions. how much is the accuracy 100% or 99.1% This file was generated by vcf-compare. T ...
beagle written 12 weeks ago by vinayreddynannuru20 • updated 12 weeks ago by zx87546.1k
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ERROR: Missing one or both alleles for a genotype:
... I have a problem when imputing with *Beagle*. In **GT** field of my VCF file I see `.` instead of `.|.`. Can someone help me in making a change of `.` with `.|.`. ...
vcf gsub impute beagle written 4 months ago by vinayreddynannuru20 • updated 4 months ago by finswimmer8.2k
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Comment: C: QUESTION: Missing genotype for Beagle imputation
... hello, i have the same problem when imputing with beagle. In GT field of my vcf file i see "." instead of .|., and i tried with the command you mentioned here but still it remains . after using that command. Can you help me in this issue. thanks, vinay kumar reddy nannuru ...
written 4 months ago by vinayreddynannuru20
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Comment: C: Error while running BEAGLE for genotype imputation
... hello, i have the same problem that there are '-' at alt column of my vcf file, how can i prefilter it. thanks, vinay ...
written 5 months ago by vinayreddynannuru20
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Comment: C: Plotting Density Of Snps On Chromosomes
... hello isran, i am vinay kumar reddy, i have vcf file of samples with different snp positions on different chromosomes, so now i want to plot this positions along chromosomes, i am trying to do it with synbreed r package and i could not succeed, can you please help me out. my vcf files consists sever ...
written 5 months ago by vinayreddynannuru20
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Comment: C: merging two different datasets of different samples and variants
... hello mr ram, yes n is two files, i have added the parameter, and my output file only contains only my project samples with similar positions of both files. But what i want is output includes all the samples from my project data and public data with similar positions. How can i do this. thanks, vina ...
written 5 months ago by vinayreddynannuru20
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Comment: C: Merging vcf files (intersection and union)
... Hello Kevin, Thank you for answer and the thing is both my project data and public data both are aligned to same reference genome already. so can i now directly proceed by merging them. thanks, vinay kumar reddy nannuru ...
written 5 months ago by vinayreddynannuru20
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Comment: C: merging two different datasets of different samples and variants
... thank you very much and i am working on it, i chose to use vcftools and when i used a command it shows folowing; vcf-isec -f -n ../vcffiles/gbs.africe.impute ../../ZeaGBSv27_publicSamples_imputedV5_AGPv4-161010.vcf Could not parse: [../vcffiles/gbs.africe.impute] at /usr/local/bin/v ...
written 5 months ago by vinayreddynannuru20 • updated 5 months ago by RamRS19k
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Comment: C: merging two different datasets of different samples and variants
... thank you very much and i am working on it. ...
written 5 months ago by vinayreddynannuru20
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[bcf_sync] incorrect number of fields (0 != 5) at 0:0 in bcftools
... Hello All, I want to compress my vcf file and always this error, '[bcf_sync] incorrect number of fields (0 != 5) at 0:0 in bcftools', what should i do here. i used following command bcftools view vcf/vcffiles/gbs.africe.impute > gbs.africa.gz Thanks, Vinay ...
bcftools written 5 months ago by vinayreddynannuru20

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