orphan: |
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- Are your target genomes and the scoring file in compatible builds?
--min_overlap
defaults to 0.75 (75% of variants in scoring file must be present in target genomes). Try changing this parameter!
Did you forget to set --max_cpu
or --max_memory?
You can also edit nextflow.config
to configure cpu and memory permanently.
pgsc_calc
bundles dependencies using containers or conda. Did you remember
to specify -profile
? e.g. nextflow run pgscatalog/pgsc_calc -profile
docker,test
Multiple profiles can be combined with a comma. The test profile is used only for checking the pipeline is installed and working correctly.
If you use a "chr" prefix in the chromosome column of your VCF, please remove it. Here's a simple method to do this (thanks to Rvtests):
(zgrep ^"#" $your_old_vcf; zgrep -v ^"#" $your_old_vcf | sed 's:^chr::ig' | sort -k1,1n -k2,2n) | bgzip -c > $your_vcf_file.gz