Tool or script to parse annotated VCF files

Question

I've annotated VCF files using snpEff and looking for a tool or script to parse the VCF file and clean up the file to make it interpretable for a biologist.

Answer 1

(edit)you can filter the VCF annotations with snpsift, I've also written a VcfFilterSequenceOntology http://lindenb.github.io/jvarkit/VcfFilterSequenceOntology.html

I've written vcf2table: http://lindenb.github.io/jvarkit/VcfToTable.html It decodes VEP and SNPeff annotations:

>>chr1/10001/T (n 1)
 Variant
 +--------+--------------------+
 | Key    | Value              |
 +--------+--------------------+
 | CHROM  | chr1               |
 (....)
 VEP
 +--------------------------+------+----------------+------------+-----------------+--------+------------------+-----------------------------------------------+-------------+---------+-----------------+----------------------+
 | PolyPhen                 | EXON | SIFT           | ALLELE_NUM | Gene            | SYMBOL | Protein_position | Consequence                                   | Amino_acids | Codons  | Feature         | BIOTYPE              |
 +--------------------------+------+----------------+------------+-----------------+--------+------------------+-----------------------------------------------+-------------+---------+-----------------+----------------------+
 | probably_damaging(0.956) | 8/9  | deleterious(0) | 1          | ENSG00000102967 | DHODH  | 346/395          | missense_variant                              | R/W         | Cgg/Tgg | ENST00000219240 | protein_coding       |
 |                          | 3/4  |                | 1          | ENSG00000102967 | DHODH  |                  | non_coding_exon_variant&nc_transcript_variant |             |         | ENST00000571392 | retained_intron      |
 |                          |      |                | 1          | ENSG00000102967 | DHODH  |                  | downstream_gene_variant                       |             |         | ENST00000572003 | retained_intron      |
 |                          |      |                | 1          | ENSG00000102967 | DHODH  |                  | downstream_gene_variant                       |             |         | ENST00000573843 | retained_intron      |
 |                          |      |                | 1          | ENSG00000102967 | DHODH  |                  | downstream_gene_variant                       |             |         | ENST00000573922 | processed_transcript |
 |                          |      |                | 1          | ENSG00000102967 | DHODH  | -/193            | intron_variant                                |             |         | ENST00000574309 | protein_coding       |
 | probably_damaging(0.946) | 8/9  | deleterious(0) | 1          | ENSG00000102967 | DHODH  | 344/393          | missense_variant                              | R/W         | Cgg/Tgg | ENST00000572887 | protein_coding       |
 +--------------------------+------+----------------+------------+-----------------+--------+------------------+-----------------------------------------------+-------------+---------+-----------------+----------------------+
 Genotypes
 +---------+------+-------+----+----+-----+---------+
 | Sample  | Type | AD    | DP | GQ | GT  | PL      |
 +---------+------+-------+----+----+-----+---------+
 | M10475  | HET  | 10,2  | 15 | 10 | 0/1 | 25,0,10 |
 | M10478  | HET  | 10,4  | 16 | 5  | 0/1 | 40,0,5  |
 | M10500  | HET  | 10,10 | 21 | 7  | 0/1 | 111,0,7 |
 | M128215 | HET  | 15,5  | 24 | 0  | 0/1 | 49,0,0  |
 +---------+------+-------+----+----+-----+---------+