Faulty rankscoring

[leahkemp]

I've noticed faulty rank scoring (carried out by the genmod score rule) on some recently analysed vcf files while using version 1.1.0 of the pipeline (singleton analysis). More specifically, I ended up with RankScore=1: in my vcf file rather than RankScore=4002:. In other words, the sample name associated with with the rankscore wasn't inserted properly. This had downstream impacts when loading a case into scout since scout seems to expect the value for RankScore in the vcf file to be associated with the value for family: in the load config.

I haven't had a chance to look into why this happened, It could be a faulty input file on my part (for example an incorrectly formatted pedigree file) and not something wrong with the code. But will open an issue in case others come across the same issue.

Will need to look into this and fix any possible issues :)

In the meantime, one hotfix (that worked for me) would be to replace those entries in the vcf file with GNU sed

sed -i 's/RankScore=1:/RankScore=4002:/g' ./vcf_annotation_pipeline/results/readyforscout/4002_filtered_annotated_readyforscout.vcf