User: biosol
biosol • 150
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Posts by biosol
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C: update genotype calls with PyVCF
... Yep! Works super fast, thanks a lot! ...
written 7 weeks ago by
biosol • 150
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... Hi everyone,
I'm parsing my vcf files with PyVCF and I would like to update my genotype calls: for every position in which the DP field is smaller than 10, genotype should be `"./."`. For the moment I've generated a list with the updated calls as I wish, like this:
vcf_reader = vcf.Reader(file ...
written 7 weeks ago by
biosol • 150
• updated
7 weeks ago by
Pierre Lindenbaum ♦ 133k
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... Hi everyone!
I would like to download 1000Genomes exome data for some African populations which I have found in [this repository][1].
However, these are only stored in `cram` format, so I was wondering if they can be found in `vcf`format somewhere else.
Any help will be appreciated. Thanks in advanc ...
written 8 months ago by
biosol • 150
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Comment:
C: PGDSPider VCF to BAYENV
... Hi Brian!
for me it was something super silly: in the population file I had spaces instead of tabs between the columns (or the other way around, I don't remember...)! Maybe it is your problem as well.
Also, I remember that I played around with the `.spid` file. For the VCF to Bayenv conversion there ...
written 8 months ago by
biosol • 150
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... Hi everyone,
I've calculated PBS values for my SNPs and now I would like to test their significance using the `qvalue` package in R.
This package asks you for either a list of p-values or (if you don't have them) to calculate them from a null distribution of your data with the function `empPvals`. M ...
written 8 months ago by
biosol • 150
0
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... And another question @JC : I have done the lift over and I'm having a look at the sequences with `UGene` (similar to `Bioedit`). I see now that a big part of panTro6 sequence is displaced just by 1 or 2 nucleotides in some regions. My next step will be to calculate the divergence between both specie ...
written 10 months ago by
biosol • 150
0
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1
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... I would like to eliminate from my human fasta those positions that don't have a match with the panTro fasta. ...
written 10 months ago by
biosol • 150
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1
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... Okey! I hadn't heard about LiftOver, but that's exactly what I need! Thank you so much! ...
written 10 months ago by
biosol • 150
1
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1
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... Hi everyone!
I'm trying to efficiently align a fasta file with a human sequence to panTro6 sequence but I'm not sure on how to avoid the gaps between both species. Are there tools that take these gaps already into account?
Thanks in advance for the help! ...
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... Thanks to both of you, you were both right!! It turns out that my `bash command` was counting both the `N's` and the header line of the sequence!! ...
written 10 months ago by
biosol • 150
Latest awards to biosol
Popular Question
8 months ago,
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For mean Tajima's D value
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8 months ago,
created a question with more than 1,000 views.
For 1000Genomes population allele frequencies for list of SNPs
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16 months ago,
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For 1000Genomes population allele frequencies for list of SNPs
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For Error: Line 2 of .ped file has more tokens than expected.
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19 months ago,
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For vcftools --TajimaD in sliding windows
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