User: kadamek49

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kadamek490
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Posts by kadamek49

<prev • 6 results • page 1 of 1 • next >
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CircosVCF test dataset?
... Hello, I would like to use CircosVCF to look at the genome and SNP density for a couple of my vcf files. However, when I submit it to be processed it gives me an error of "Upload faild. This may happen if the chromosomes included in the karyotype have no SNP data in the VCF files." I am unsure of ...
circosvcf vcf test dataset example written 7 days ago by kadamek490
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A method to count genotype ALT amounts for a vcf file with 3 samples?
... Hello, I have a vcf file with 3 different samples that are compared to the reference genome. I am looking for a way to count the ALT genotypes that appear for each sample. But I would like to take this a step further by using some code to look into the accumulating variants. Thus, I would like to ...
gene vcf sequence genome written 4 weeks ago by kadamek490
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Vcf file with 3 samples and trying to count variants
... Hello, I have a vcf file with 3 samples from the same plant (bot, mid, top sections were sequenced) and I am trying to look into any accumulated mutations that were possibly carried on from the bottom to top samples. I was able to find the number of ALT for each sample independently with the code b ...
vcf genome sequencing gene count written 5 weeks ago by kadamek490
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Vcf file with 3 samples and trying to count how many mutations for each sample
... Hello, I have a vcf file and want to find the counts for how many variants are occurring for each of the 3 samples independently. I have a vcf that shows the different variants between the samples (ex. 0/1 0/0 1/1 vs 0/1 0/1 0/1). I have tried some of the code and help from other posts but nothing ...
vcf snpeff bcftools written 6 weeks ago by kadamek490 • updated 4 days ago by Biostar ♦♦ 20
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Comment: C: Vcf filtering GT for between sample variants only
... Thank you! This worked and accomplished what I was asking. Really appreciate it! ...
written 3 months ago by kadamek490
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Vcf filtering GT for between sample variants only
... Hello, I have a vcf file with 3 samples and would like to filter genotype(GT) variants that are the same across all 3 samples (Ex. 0/1 0/1 0/1). I am looking for differences between the 3 samples and want only variants that are different between the 3 samples (Ex. 0/0 0/0 0/1). Most of my genotypes ...
vcf heterozygous vcftools snp written 3 months ago by kadamek490

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