gtc2vcf
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freeseek
Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
Hello, freeseek, I cannot seem to convert my .gtc files to a vcf file using the following code: bpm_manifest_file="InfiniumOmni2-5-8v1-5_A1.bpm" csv_manifest_file="InfiniumOmni2-5-8v1-5_A1.csv" egt_cluster_file="InfiniumOmni2-5-8v1-5_A1_ClusterFile.egt" ref="$HOME/GRCh37/human_g1k_v37.fasta" out_prefix="batch1_vcf" bcftools +gtc2vcf --no-version -Ou --bpm $bpm_manifest_file --csv...
I will want to used idat file more than gtc, do you have an example of command line? `bcftools +gtc2vcf -Ou --bpm .bpm --egt egt --idat filelink --fasta-ref fasta --extra...
After I install bcftools, I follow the README document and run the following code, but there is a error message. `path_to_output_folder="..." cel_list_file="..." apt-probeset-genotype \ --analysis-files-path . \ --xml-file GenomeWideSNP_6.apt-probeset-genotype.AxiomGT1.xml \...
hi, devoloper. After I install bcftools-1.11 and gtc2vcf, I run the following code `/data_6t/lizhan/02.software/bcftools-1.11/bcftools +affy2vcf \ --no-version -Ou \ --csv $csv_manifest_file \ --fasta-ref $ref \ --chps $path_to_chp_folder \ --snp $path_to_txt_folder/AxiomGT1.snp-posteriors.txt...
Hi thanks for the great tool. I have some query, I want to remove some poor quality snps from the vcf file. The filteration I want should be based the...
Hello, and thanks for a great tool! I am working on some older genotype data (on the PsychChip) where the IDAT files have unfortunately been lost to time, but where...
Hi, I am compiling a data catalog for my department where the data set span 27+ manifests which come from different times some of them pre-2009 era. Many of these...
Hello, may I have any questions here? The permissions for the file are all turned on
Hello, I tried a simple test with a cel but it segfaults. Am I doing it wrong or what might cause the issue? bcftools +affy2vcf -v --csv GenomeWideSNP_6.na35.annot.csv --fasta-ref human_g1k_v37.fasta...
Hello - Thank you for this tool for converting IDAT files into usable vcf files for analysis in plink. It's terrific! I recently ran into an issue that I cannot...