User: Wietje

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Wietje60
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Posts by Wietje

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Phasing without a reference panel
... As far as I know, you have to invoke the reference panel option with --input-ref to make use of such a panel - otherwise SHAPEIT will phase without this kind of background information. If you want to use the 1000GP data for your phasing step, you'd have to download it as described on the SHAPEIT pag ...
written 2 days ago by Wietje60
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Comment: C: Phasing without a reference panel
... And you might want to take a look at SHAPEIT as well (http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html)... ...
written 10 days ago by Wietje60
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Answer: A: Phasing without a reference panel
... Beagle 4.0 offers the option to impute and phase without a reference panel You should be able to run it with: java -jar ./beagle gt=[your.file.vcf] phase-its=5 nthreads=1 out=[your.output] You can speed up the process with more threads and improve phasing accuracy by augmenting the phase-its numb ...
written 10 days ago by Wietje60
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Answer: A: when a contig is called "orphan"?
... I suppose "orphan contigs" simply refers to contigs that were constructed from orphan reads, i.e. reads that could not be mapped (to the reference genome). Does this help you? ...
written 23 days ago by Wietje60
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Comment: C: vcftools/ plink conserve phase information
... Yes, I switched to bcftools for tha t- and vcf-subset also seems to do the job - thanks for the idea though! ...
written 26 days ago by Wietje60
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vcftools/ plink conserve phase information
... Hello fellow Biostars, I would like to **extract** a set of samples from a very large **VCF file** that already contains phase information. However, when I extract individuals with the option --keep in either PLINK or vcftools, the phase information is lost in the new subset. Is there a way to avoi ...
phase information haplotype plink vcftools written 4 weeks ago by Wietje60 • updated 4 weeks ago by chrchang5232.9k
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Answer: A: Plink. Convert ped files of artificially mixed population into vcf using recode
... The options recoding options influence how the sample ID in the VCF file is composed, check the PLINK manual or this link for that: > "The 'vcf', 'vcf-fid', and 'vcf-iid' modifiers result in production of > a VCFv4.2 file. 'vcf-fid' and 'vcf-iid' cause family IDs and > within-family IDs re ...
written 6 weeks ago by Wietje60
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Answer: A: From Impute2 to PLINK: when to merge chromosome files?
... I suppose it is safe to convert them in PLINK and then apply merge. I recommend the merge-list option which allows you to merge several files in one go. ...
written 6 weeks ago by Wietje60
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Comment: C: imputation and changing genotypes in Beagle and FImpute
... Thank you for the suggestion, I will look into it for sure - unfortunately, this does not answer my initial question though... ...
written 10 weeks ago by Wietje60
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imputation and changing genotypes in Beagle and FImpute
... Hello fellow Biostars, I am currently aiming to impute genotypes from different SNP-Chip resolutions (6k, 50k, 777k...) and have tried Beagle 4.0 and FImpute because I want to include pedigree information. The process seems successful so far, however, **FImpute** notifies me that changes to the o ...
beagle 4.0 fimpute imputation genotypes written 10 weeks ago by Wietje60 • updated 10 weeks ago by Shab86220

Latest awards to Wietje

Scholar 5 days ago, created an answer that has been accepted. For C: Bedtools intersect QTL animalgenome
Scholar 7 months ago, created an answer that has been accepted. For C: Bedtools intersect QTL animalgenome

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