User: b.ambrozio

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b.ambrozio20
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Posts by b.ambrozio

<prev • 12 results • page 1 of 2 • next >
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How to run BOLT-LMM against a Plink simulated dataset?
... I'm trying run [BOLT-LMM][1] against a simulated dataset, which were generated with [plink --simulate][2], however no success: ./BOLT-LMM_v2.3.4/bolt --bfile=ds1_1gt10k --phenoUseFam --statsFile ds1_1gt10k.bolt --LDscoresUseChip --lmm ... ERROR: LOCO mixed model analysis requires >= ...
plink bolt-lmm written 3 months ago by b.ambrozio20
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How to extract the classification/regression metrics from a GWAS so that I can compare different tools?
... If I understood well, GWAS is pretty much a feature selection approach based on a classification or regression algorithm, whenever the underlying trait is qualitative or quantitative, respectively. My question is, how can I extract the classification/regression metrics from the executed GWAS algori ...
gcta saige metrics plink bolt-lmm written 4 months ago by b.ambrozio20
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How to simulate phenotype from real genetic data for GWAS purpose?
... I'm trying to simulate binary phenotypes from the [1000 Genome Phase 3 datasets][1] using [gcta64 --simu-cc][2], but no success. Everything seems to be going well, but in the end I get: Error: can not open the file [] to read. An error occurs, please check the options or data And the log ...
plink gcta written 4 months ago by b.ambrozio20 • updated 4 months ago by jian.yang.qt30
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Answer: A: how to remove multiallelic from VCF
... I was trying to do the same with all the 22 VCFs of the [1000 genome phase 3 datasets][1] (~15G compressed) concatenated in a single VCF, but with `bcftools` was taking hours (more than 10 hours and still running). This is the command I was trying: vcf_file=../../ALL.phase3_shapeit2_mvncall_int ...
written 4 months ago by b.ambrozio20
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Comment: C: How to convert VCF to CSV?
... Well, I guess not. Actually I've reduced the scope to 3 chromosomes, and removed the "D", thus I managed to generate. But now I'm facing issues to load it and work on my pandas, pySpark, etc... I think I have to change the strategy, and try to, some how, run my classification models straight from th ...
written 5 months ago by b.ambrozio20
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How to convert VCF to CSV?
... How can I convert VCF to CSV, so that I can use it in a classification model? I'm trying to convert the [1000 genome phase 3 data](2) to a CSV using plink, but no success, as I'm getting the error: `Error: --export AD header line too long (>2GiB).`. Here's the details: $ du -cah 14G ...
vcf csv plink written 5 months ago by b.ambrozio20 • updated 5 months ago by chrchang5237.1k
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Comment: C: How to simulate 100k samples having 40 million SNPs in a proportion of case:cont
... Sorry about that. I'm new on bioinformatics, not sure which community should I use... ...
written 6 months ago by b.ambrozio20
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How to simulate 100k samples having 40 million SNPs in a proportion of case:control=30:70?
... Hi there, I need to perform a stress test in a GWAS tool and the duty demands a dataset (plink format) having 100 thousand samples, having 40 million SNPs in a proportion of case:control=30:70. I'm performing the command: plink1.9 --simulate ds1.sim --make-bed --out ds1 --simulate-ncases 300 ...
gwas plink written 6 months ago by b.ambrozio20 • updated 6 months ago by zx87549.4k
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What is the state of the art for GWAS in terms of statistical algorithm for either Case/control and Quantitative traits?
... Hello! I'm trying to understand what is the best algorithm for GWAS nowadays. I know we have many tools available like Plink and Hail, but currently, what is the best algorithm if I won't use any them? Let's say, write down a script in R or Python from scratch. Which statistical algorithm should I u ...
gwas lmm written 8 months ago by b.ambrozio20 • updated 8 months ago by chrchang5237.1k
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Answer: A: Any fast way to download 1000 Genome Phase 3?
... Ok, I got it working. The change was pretty much the `-i` parameter that in my case had to be for the new version of the `ascp`: `asperaweb_id_dsa.putty`. That's funny as yesterday I'm pretty sure I tried and didn't work (error "Too many authentication failures". I'm guessing the credential were blo ...
written 9 months ago by b.ambrozio20

Latest awards to b.ambrozio

Scholar 9 months ago, created an answer that has been accepted. For A: Any fast way to download 1000 Genome Phase 3?

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