Nikki Lukasko
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Activity overview
Latest activity by Nikki Lukasko-
Nikki Lukasko commented,
Hi again Gökalp Çelik I am trying to see if this is the result of heterokaryotic behavior (2 genetically distinct nuclei in the same cell) in a haploid organism. It is a long story, but other evide...
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Nikki Lukasko commented,
Hi Gökalp Çelik, Here is a small snippet from igv showing read depth, but I can tell that there are heterozygous reference and heterozygous alternate variants in the bam files. I think this is what...
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Nikki Lukasko commented,
Hi Gökalp Çelik Here are the commands I used to generate the vcf: ``` gatk-4.2.5.0/gatk --java-options "-Xmx100g" HaplotypeCaller -R ref.fa -ERC GVCF -I /Plates23/A_B/${base}.bam -O /${base}_aln_HC...
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Nikki Lukasko commented,
Hello SkyWarrior, sorry for the delayed response. There is not any conflicting data in my vcf, but rather the absence of entries I expected to see. I searched my vcf (276 whole-genomes) using the f...
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Nikki Lukasko commented,
SkyWarrior Assuming the allelic depth is always reported in the order of reference [0], alternate [1]: I find it odd that regardless of the genotype called, the first number is always lower than th...
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Nikki Lukasko commented,
Hi SkyWarrior, Thank you for a quick response. I understand the likelihood portion, but am still curious about which read depth corresponds to each genotype. I made up the second example but am sti...
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Nikki Lukasko created a post,
VCF allelic depth (AD) supports the reference or alternate?
I used GATK 4.2.5 HaplotypeCaller to generate vcfs for my samples. I called them as haploids and and am looking for clarification regarding allelic depth. The format is as follows:GT:AD:DP:GQ:PL 1:...