Major revision. Added filters to get InDels and Splicing sites. Added a VCF based frequency filter at default 0.5 to remove common variants that are unannotated in 1kg or ESP. Add filters for quality based on FILTER field so that it can be run on unfiltered vcf, different for Indels and SNPs. A few changes to the output and removed a few redundant lines of code.
Changed job name
Removed de novo filter and changed AD echo
Updated deleterious prediction filter handling. Added a column to output med or high based on predictions. Add nonsense to high class
Updated to remove stringent/relaxed calls
Script to filter a VCF for variants with an alternate allele - for use after subsetting a vcf by sample
Added options to output unfiltered individuals genotypes, allow a more relaxed de novo calling, add any addtional parameters to the filter script call
Removed -p parameter for pathogenecity level
Removed -p parameter for pathogenecity level
Removed -p parameter for pathogenecity level
Added line to match the genotype columns of the two tsvs.
Major update. Added obligate filtering of splice sites, indels, and nonsense. Added GERP++ and full atlernate allele columns to output. Relaxed filteres DP 5 --> 3, and GQ 40 --> 30. Added heterozygous alternate allele count filter - min 3 default. Added homozygous allele fraction filter - min 0.8 default. Added -D to change defaults to more stingent level for de novos. Added -Q to filter without using vcf FILTER field. Updated output to log.
Added ignore - TEST*