User: GabrielMontenegro

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Posts by GabrielMontenegro

<prev • 117 results • page 1 of 12 • next >
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Subsetting individuals in PLINK when IDs contain underscores "_"
... I am working with a VCF dataset and many individuals have IDs including an underscore. I want to subset them using plink, but I keep getting this error: Error: More than two instances of '_' in sample ID. Is there a way for plink to ignore the underscores in those IDs and treat them as a sing ...
plink written 20 days ago by GabrielMontenegro330 • updated 20 days ago by pfs90
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Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... Thanks - that worked! ...
written 29 days ago by GabrielMontenegro330
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Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... So then: `... --ref-allele force ancestral_snps.txt 1 2 ...`. Would this work? Thanks again. ...
written 5 weeks ago by GabrielMontenegro330
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Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... So if I understand correctly, the `--ref-allele force` will make the specified (in this case ancestral) alleles be changed to 0? I am checking the help page, but I am not sure what this means: `{refcol} {IDcol} {skip}` ? What column numbers would I need to specify? Is it from the VCF or the `ancestr ...
written 5 weeks ago by GabrielMontenegro330
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Comment: C: Kinship Relatedness using plink
... Check how PI_HAT is computed in PLINK, specially how IBD is calculated. You will then see that this estimates can be affected for instance by admixture/consanguinity. For example, if your population is highly drifted and/or has experienced various bottlenecks (think of Native Americans say) a PI_HAT ...
written 5 weeks ago by GabrielMontenegro330
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Comment: C: Kinship Relatedness using plink
... I suggest you to check out this previous post: https://www.biostars.org/p/75335/ ...
written 5 weeks ago by GabrielMontenegro330
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Forcing A1/A2 alleles in PLINK in a VCF phased file
... I have a phased VCF file and I need to change the alleles of the SNPs so that the alleles coded as 0 represent the ancestral state while the alleles coded as 1 represent the derived state. I got a list of ancestral and derive states for my SNPs in my VCF file and I want to change them using PLINK. ...
vcf plink snp written 5 weeks ago by GabrielMontenegro330
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Comment: C: 1000 genomes PCA for whole genome
... PLINK can handle VCF files. The problem as Sam mentioned is that you will first need to exclude multi-allelic sites. Also, before doing a PCA, you will have to remove SNPs on LD (i.e. prune your data). You can use the `--indep` or `indep-pairwise` function in PLINK too. ...
written 5 weeks ago by GabrielMontenegro330
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Merging inconsistencies in PLINK
... I am trying to merge two different PLINK files genotyped on the same platform. However, I found some inconsistencies that could not be solved by the `--flip` command. I checked the SNPs that could not be merged after the flip and found this type of problem: File 1: 4 rs10000432 68.93 ...
plink snp written 5 weeks ago by GabrielMontenegro330
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Comment: C: How to estimate significance of RPKM value on GTEX
... Reading the GTEX Science paper (http://science.sciencemag.org/content/348/6235/648/tab-pdf) I have seen that they mention a "minimal treshold reads per kilobases per millon mapped reads (RPKM) > 0.1". Does this mean that in order to say that a tissue is expressed needs to have at least 0.1 RPKM? ...
written 9 weeks ago by GabrielMontenegro330

Latest awards to GabrielMontenegro

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Popular Question 5 months ago, created a question with more than 1,000 views. For Using Ldhat To Estimate Effective Population Size
Student 5 months ago, asked a question with at least 3 up-votes. For Good books to learn probability distributions
Scholar 7 months ago, created an answer that has been accepted. For A: How to convert input files from PLINK to snp.plotter?
Popular Question 7 months ago, created a question with more than 1,000 views. For Using Ldhat To Estimate Effective Population Size
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Popular Question 10 months ago, created a question with more than 1,000 views. For Changing Build From 37 To 36 In Snp Data
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