Comments (2)
It seems there is a problem with the query file, and that there is a place in the code I need to add output for an error message.
To get the message that is suppressed, could you run this command (the preprocess binary should be deployed in the same place as hap.py):
QUERY.vcf.gz should be bgzipped and indexed (or a bcf file with corresponding csi index, if not, preprocess will fail):
preprocess QUERY.vcf.gz:* -l 4:46200230-49670140 -o test.vcf.gz -V 1 -L 0 -r /ssd/reference/fda/nih.GRCh37.fasta
This command should fail as above, but also output a message telling us why. I'll add error output for this case to the to-do list in hap.py 0.3.7
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This should be fixed in v0.3.7 now.
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Related Issues (20)
- Parsing results VCF gives different counts of TRUTH FN than summary HOT 1
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- missing reference HOT 1
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