MAF filter not working in v-view

[Arthur Goldberg]

All of these commands fail to apply the MAF filter. That is, they return a .vars file with variants with maf>0.05.

pseq TADA_analysis v-view --only-alt --mask maf=0-0.05 filter.req=PASS --vmeta --show AF SNPEFF_EFFECT --out TADA_analysis

pseq TADA_analysis v-view --only-alt --mask maf=0-0.05 filter.req=PASS --vmeta --show AF SNPEFF_EFFECT --geno --out TADA_analysis

pseq TADA_analysis v-view --only-alt --mask maf=0-0.05 filter.req=PASS meta.req=SNPEFF_EFFECT:is:SYNONYMOUS_CODING,SNPEFF_EFFECT:is:NON_SYNONYMOUS_CODING,SNPEFF_EFFECT:is:SPLICE_SITE_ACCEPTOR,SNPEFF_EFFECT:is:SPLICE_SITE_DONOR,SNPEFF_EFFECT:is:EXON_DELETED,SNPEFF_EFFECT:is:FRAME_SHIFT,SNPEFF_EFFECT:is:STOP_GAINED reg=@/tmp/tmp.onXIrlgU9u indiv=@/tmp/tmp.jWruBpqPxo --vmeta --show AF SNPEFF_EFFECT --geno --out TADA_analysis

$ pseq x version PSEQ: 0.09 PSEQ DATE: 8-Oct-13 LOCDB: 3 PLINKSEQ: 0.09(8-Oct-2013) PROJN_SPEC_FILE: 2 REFDB: 3 SQLITE3_HEADER: 3.8.0.2 SQLITE3_LIBRARY: 3.8.0.2 VARDB: 5 VCF: VCFv4.1 ZLIB: 1.2.3

Happy to provide example pseq project if that would help. Arthur