How to export a matrix table as a VCF file after annotation on UKB RAP using HAIL?
I want to export my annotated matrix table as a vcf file as I want to filter my variants on my own server and not on DNAnexus. In order to export as a vcf I had to manually select which annotations I would like in the info field using this code:
annotated_mt = annotated_mt.annotate_rows(info=annotated_mt.info.annotate(CADD_PHRED=annotated_mt.CADD[?PHRED_score?]))
However, when I try exporting as a VCF I get the following error:
Error summary: VCFParseError: unexpected end of line
I can export as a.tsv file from a hail table but this does not contain the genotype information so it makes it a bit trickier for variant filtering. As well as this, some annotations were not inputted into the info field as simple strings or floats and could not be exported. Example:
annotated_mt = annotated_mt.annotate_rows(info=annotated_mt.info.annotate(gnomAD_pLI = annotated_mt.dbNSFP_genes[?gnomAD_pLI?]))
Just wondering if there is a simpler way to export annotations in a VCF file for variant filtering.
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According to Annex 1 of MTA that your institution signed with UKB, all the WES and WGS must not be transmitted or downloaded from the research analysis platform.
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