User: biosol

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biosol150
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Posts by biosol

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Comment: C: update genotype calls with PyVCF
... Yep! Works super fast, thanks a lot! ...
written 7 weeks ago by biosol150
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update genotype calls with PyVCF
... 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 ...
pyvcf genotypes written 7 weeks ago by biosol150 • updated 7 weeks ago by Pierre Lindenbaum133k
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1000Genomes exome vcf
... 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 ...
vcf 1000genomes exome written 8 months ago by biosol150
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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 biosol150
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qvalue for PBS
... 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 ...
R qvalue pbs written 8 months ago by biosol150
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Comment: C: align specific region of human to panTro6
... 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 biosol150
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Comment: C: align specific region of human to panTro6
... 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 biosol150
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Comment: C: align specific region of human to panTro6
... Okey! I hadn't heard about LiftOver, but that's exactly what I need! Thank you so much! ...
written 10 months ago by biosol150
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align specific region of human to panTro6
... 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! ...
pantro6 alignment written 10 months ago by biosol150 • updated 10 months ago by JC12k
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Comment: C: twoBitToFa retrieving longer sequence than expected in hg19
... 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 biosol150

Latest awards to biosol

Popular Question 8 months ago, created a question with more than 1,000 views. For mean Tajima's D value
Popular Question 8 months ago, created a question with more than 1,000 views. For 1000Genomes population allele frequencies for list of SNPs
Popular Question 16 months ago, created a question with more than 1,000 views. For 1000Genomes population allele frequencies for list of SNPs
Popular Question 19 months ago, created a question with more than 1,000 views. For Error: Line 2 of .ped file has more tokens than expected.
Popular Question 19 months ago, created a question with more than 1,000 views. For vcftools --TajimaD in sliding windows

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