What it does
Filter LoF variants by transcript position and type
Not all candidate LoF variants are created equal. For e.g, a nonsense (stop gain) variant impacting the first 5% of a polypeptide is far more likely to be deleterious than one affecting the last 5%. Assuming you’ve annotated your VCF with snpEff v3.0+, the lof_sieve tool reports the fractional position (e.g. 0.05 for the first 5%) of the mutation in the amino acid sequence. In addition, it also reports the predicted function of the transcript so that one can segregate candidate LoF variants that affect protein_coding transcripts from processed RNA, etc.
Output with default settings:
chrom start end ref alt highest_impact aa_change var_trans_pos trans_aa_length var_trans_pct sample genotype gene transcript trans_type chr22 17072346 17072347 C T stop_gain W365* 365 557 0.655296229803 NA19327 C|T CCT8L2 ENST00000359963 protein_coding chr22 17072346 17072347 C T stop_gain W365* 365 557 0.655296229803 NA19375 T|C CCT8L2 ENST00000359963 protein_coding chr22 17129539 17129540 C T splice_donor None None None None NA18964 T|C TPTEP1 ENST00000383140 lincRNA chr22 17129539 17129540 C T splice_donor None None None None NA19675 T|C TPTEP1 ENST00000383140 lincRNA