README.md

Seqant 2.0

Annotator Output

Some seqant output columns are found regardless of the included tracks

1. chrom

   • The chromosome name (chr1, chr2, etc)

2. pos

   • The position. For deletions this is the first base deleted, for insertions this is the base just before the insertion.
   • This is different from VCF spec, and much less complicated

3. type

   • The variant call.
   • Possibilities: SNP, INS, DEL, MULTIALLELIC, DENOVO_SNP, DENOVO_INS, etc.

4. discordant

   • Whether the assembly matches the reference alelle given by the user's input file.

5. alt

   • The alternate allele(s). This is taken directly from the input file.heterozygotes

6. homozygotes

   • If the sample has the given allele single-copy.
   • In multiallelic case, phased on allele

7. heterozygotes

   • If the sample has the given allele in copy nunmber matching the # of chromosomes
   • In multiallelic case, phased on allele

The Seqant configuration file

• The config file describes the state of both the database and the annotation. It's required for annotating or buildign
• It has several keys:
• tracks: What your database contains, and what you annotate against. Tracks have a name, which must be unique, and a type, which doesn't need to be unique
  • type: A track needs to have a type
    • sparse: Accepts any bed file, or any file that has at least a valid chrom, chromStart, and chromEnd. We can transform almost any file to fit this format, TODO: give example below.
    • score: Accepts any wigFix file.
      • Used for phastCons, phyloP
    • cadd: Accepts any CADD file, or SeqAnt's custom "bed-like" CADD file (TODO: DESCRIBE)
      • CADD format: http://cadd.gs.washington.edu
    • gene: A UCSC gene track, either knownGene, or refGene. The "source files" for this is an sql_statement key assigned to this track (described below)

Directories and Files

These describe where the Seqant database and any source files are located.

1. files_dir : Where our source files are located. This is only necessary when building a new database

Ex:

files_dir: /path/to/files/

2. database_dir : Where the database is located. Required

database_dir: /path/to/database/