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freeseek / gtc2vcf

Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
MIT License
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Failed to open file "Ou" : No such file or directory #49

Closed crbeam closed 1 year ago

crbeam commented 2 years ago

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 $csv_manifest_file --egt $egt_cluster_file --gtcs $path_to_gtc_folder --fasta-ref $ref --extra $out_prefix.tsv | bcftools sort -Ou -T ./bcftools-sort.XXXXXX | bcftools norm --no-version -Ob -c x -f $ref | tee $out_prefix.bcf | bcftools index --force --output $out_prefix.bcf.csi

The error that I receive is [E: :hts_open_format] Failed to open file "Ou" : No such file or directory Reading BPM file InfiniumOmni2-5-8v1-5_A1.bpm Could not read Ou Failed to read from standard input: unknown file type index: "-" is in a format that cannot be usefully indexed

I've tried adapting the command by reading through the other issues that have come up, but have had no luck creating a bcf file that has > 0 bytes. May I ask for assistance in resolving this issue? I should mention that the manifest and cluster files provided by illumina are in the same directory in which I am running this command.

Thank you, Chris

crbeam commented 2 years ago

Please disregard. A dash (-) before "Ou" in the bcftools sort command was missing. Thanks for a nice set of tools. Chris