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Illumina / hap.py

Haplotype VCF comparison tools
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missing reference #174

Closed Overcraft90 closed 1 year ago

Overcraft90 commented 1 year ago

Hi there,

I'm running hap.py with the following command:

sudo docker run -it -v `pwd`:/data /opt/hap.py/bin/hap.py /data/output/HG002-output_happy.vcf.gz /data/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz -r /data/hg38_graph_happy.fa -o /data/0.SNPs_eval

however, I keep getting a message similar to this #83. I'm using my own reference, and I even tried to set:

export HGREF=/media/scratch/DeepVariant/input/hg38_graph.fa

but, unfortunately, I couldn't get the tool to work... Any idea on what should cause this? Thanks in advance!

Overcraft90 commented 1 year ago

Actually, the solution was to get rid of the folder named 0.SNPs_eval since hap.py uses the string after the -o flag as a prefix to its output files. Sorry, my mistake I must have missed it while reading the help.