User: dylkot

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dylkot0
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Posts by dylkot

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Answer: A: Is there a tool to transform GenomeStudio genotype format to VCF?
... As far as I can tell the pipeline described above is the main way to do this: GenomeStudio --(PLINK plugin)--> PLINK .ped file --(PLINK to vcf function)--> VCF. My only complaint about it is that PLINK swaps the allele order so that A2 is always major and so it won't preserve REF/ALT informati ...
written 12 weeks ago by dylkot0
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Comment: C: Merging variant replicates rather than filtering
... Also, as a quick note, the command: plink --bmerge inputdata --bfile inputdata --merge-equal-pos --out outputdata fails when (as in my case), variants and the same position are replicates and in other cases, they are multi-allelic variants and so have different ALT alleles. ...
written 6 months ago by dylkot0
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Comment: C: Merging variant replicates rather than filtering
... Thanks for the tip! Are you referring to the --merge-equal-pos option in PLINK 1.9? If so, do you know how it performs the merge? The documentation is ambiguous stating: If two variants have the same position, PLINK 1.9's merge commands will always notify you. If you wish to try to merge them, use ...
written 6 months ago by dylkot0
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Merging variant replicates rather than filtering
... I'm analyzing some Illumina genotype data and noticing that almost 2% of variants on the array are typed more than once. I consider these measurements to be replicate if they are measuring the same chromosome, position, reference allele, and alternate allele as specified in the PLINK BIM file. It se ...
gwas plink vcftools written 6 months ago by dylkot0 • updated 6 months ago by chrchang5234.8k
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Comment: C: Reversing direction of chain files (E.g. from hg18-->hg19 to hg19-->hg18)
... Thanks for the clarification. So if I understand correctly, the issues relate both to the specific implementation of alignment used to generate the chain files, errors in the officially sanctioned sequences, and incompatibilities due to lack of contiguity information for repeated segments.    I th ...
written 4.0 years ago by dylkot0
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Comment: C: Reversing direction of chain files (E.g. from hg18-->hg19 to hg19-->hg18)
... Hi Brian,   Thanks for for your response. Perhaps I'm misunderstanding but isn't it the case that any feature that is present in 1 reference but not the other can be represented in a chain file by a gap? It still seems to me like the same interval pairings should exist in the reversed file.   ...
written 4.0 years ago by dylkot0
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Reversing direction of chain files (E.g. from hg18-->hg19 to hg19-->hg18)
... I need to convert a chain file that allows liftover from one reference to another (reference X-->Y) to one that would permit the reverse liftover (reference Y-->X). I thought that this would be as simple as swapping the second and third columns and making the corresponding adjustment to the he ...
alignment chain files liftover written 4.0 years ago by dylkot0 • updated 4.0 years ago by Brian Bushnell16k

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Popular Question 3.9 years ago, created a question with more than 1,000 views. For Reversing direction of chain files (E.g. from hg18-->hg19 to hg19-->hg18)

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