Yanranli007

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imp5Converter Output file format is not supported

I have the same problem, pfx="ALL.chr" sfx=".phase3_integrated.20130502.genotypes" for chr in {{1..22},X}; do $imp5Converter_PATH --h $WORK37/$pfx$chr$sfx.bcf --o $WORK37/$pfx$chr$sfx.**imp5** --r $chr done When I add the imp5, it works, I think you...

imp5Converter Output file format is not supported

> > I have the same problem, pfx="ALL.chr" sfx=".phase3_integrated.20130502.genotypes" > > for chr in {{1..22},X}; do $imp5Converter_PATH --h $WORK37/$pfx$chr$sfx.bcf --o $WORK37/$pfx$chr$sfx.**imp5** --r $chr done > > When I add the...

imp5Converter Output file format is not supported

> I realized this is legacy code from version 1.1.5 of IMPUTE5. With the newer 1.2.0 version the `imp5Converter` bianry should be replaced by the `xcftools` binary and the code...

Can I Use CEL Files from Axiom Precision Medicine Research Array (PMRA) Release 3 to Generate CHP Files and Obtain VCF Files Annotated with GC, BAF, and LRR Content?

> I am not sure but I don't think it is possible to generate CHP files for Axiom PMRA. But you can generate .calls.txt/.confidences.txt/.summary.txt/.snp-posteriors.txt files and convert them to VCF...

Can I Use CEL Files from Axiom Precision Medicine Research Array (PMRA) Release 3 to Generate CHP Files and Obtain VCF Files Annotated with GC, BAF, and LRR Content?

> It seems like all the online documentation has been taken offline by Thermofisher. But you can still download the [Analysis Power Tools](https://www.thermofisher.com/it/en/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-network/affymetrix-power-tools.html) and look into the file `doc/vignette-axiom-probeset-genotype.html` for...

Can I Use CEL Files from Axiom Precision Medicine Research Array (PMRA) Release 3 to Generate CHP Files and Obtain VCF Files Annotated with GC, BAF, and LRR Content?

Dear Dr. Genovese, Under your guidance, I successfully converted various file types (.calls.txt, .confidences.txt, .summary.txt, and .snp-posteriors.txt) into a standardized VCF format incorporating GC, LRR, and BAF values, and have...

Can I Use CEL Files from Axiom Precision Medicine Research Array (PMRA) Release 3 to Generate CHP Files and Obtain VCF Files Annotated with GC, BAF, and LRR Content?

Dear Dr. Genovese, When I changed the version to IMPUTE5 v1.1.5. This process worked. However, I've noticed that the process still requires a significant amount of memory and CPU resources,...

Can I Use CEL Files from Axiom Precision Medicine Research Array (PMRA) Release 3 to Generate CHP Files and Obtain VCF Files Annotated with GC, BAF, and LRR Content?

> IMPUTE5 v1.2.0 is much more memory efficient than IMPUTE5 v1.1.5. Nevertheless, the author discourages using it across whole chromosomes and it should always be run over chromosome chunks. This...