User: freeseek

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freeseek100
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Posts by freeseek

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Comment: C: What reference build are affymetrix 5.0 arrays?
... Agreed and feel free to delete these old posts if you think it is impossible to get feedback from the right users. As soon as I will get a bit of feedback myself knowing that the tool satisfies most use cases I will post it as a tool. Thank you ATpoint and genomax for your suggestions! :-) ...
written 11 months ago by freeseek100
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Comment: C: What reference build are affymetrix 5.0 arrays?
... Thank you for your suggestion ATpoint. The problem is that these posts, despite old, come up in Google searches when using the right keywords and often have no satisfactory answer (such as this one). I just did not want users to end up on these questions and find no solution. I am just trying to hel ...
written 11 months ago by freeseek100
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Answer: A: What reference build are affymetrix 5.0 arrays?
... I would advise to use the [affy2vcf][1] bcftools plugin to convert the original raw CEL files to VCF rather than trying to convert PLINK data to VCF which is not recommended. Notice that affy2vcf will also allow you to remap the array manifest to GRCh38 or other human genome reference of your choice ...
written 11 months ago by freeseek100
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Answer: A: SNP array CNV calling for Cancer tissue (.CEL files)
... If you are interested in clonality, you can use the [affy2vcf][1] bcftools plugin to convert the apt-probeset-genotype output to VCF and then use the [MoChA][2] pipeline to call mosaic chromosomal alterations arising from clones [1]: https://github.com/freeseek/gtc2vcf [2]: https://github.com/f ...
written 11 months ago by freeseek100
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Answer: A: conversion from CEL file to PLINK format (.map, .ped)
... You can use the [affy2vcf][1] bcftools plugin to convert the apt-probeset-genotype output to VCF and then use [best practices][2] to convert the VCF output to PLINK. I believe this is the fastest way [1]: https://github.com/freeseek/gtc2vcf [2]: http://apol1.blogspot.com/2014/11/best-practice-f ...
written 11 months ago by freeseek100
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Answer: A: How to convert and annotate apt-probeset-genotype into PLINK format
... You can use the [affy2vcf][1] bcftools plugin to convert the apt-probeset-genotype output to VCF and then use [best practices][2] to convert the VCF output to PLINK format or easily perform the quality control on the VCF file using bcftools [1]: https://github.com/freeseek/gtc2vcf [2]: http://a ...
written 11 months ago by freeseek100
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Answer: A: Get Genotypes From Affymetrix Snp 6.0 Array
... You can use the [affy2vcf][1] bcftools plugin. You will only need to run the apt-probeset-genotype software from APT, which is fast. Then you can easily convert the TXT output to VCF with both genotypes and confidence scores [1]: https://github.com/freeseek/gtc2vcf ...
written 11 months ago by freeseek100
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Answer: A: Illumina Manifest files - A1 vs. A2
... I have found that it is always the case that _A1, _B1, _C1 manifest files contain GRCh37 mappings and _A2, _B2, _C2 manifest files contain GRCh38 mappings. If you don't have an _A2, _B2, _C2 manifest file, you can remap the flanking sequences against GRCh38 using [gtc2vcf][1] [1]: https://github. ...
written 11 months ago by freeseek100
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Answer: A: Is there an allternative to Affymetrix GTC for Genotyping?
... You can use the apt-probeset-genotype software as explained [here][1] with the additional option --cc-chp-output to generate single sample .CHP files with genotype calls. It works on Linux and it should work on Mac as well. [1]: https://github.com/freeseek/gtc2vcf ...
written 11 months ago by freeseek100
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Answer: A: Automate Illumina GenomeStudio With Python Script
... Nowadays all of this can be done on the command line without using GenomeStudio as explained [here][1] [1]: https://github.com/freeseek/gtc2vcf ...
written 11 months ago by freeseek100

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