Quick start:

git clone --recursive https://github.com/Cibiv/BODscore

cd BODscore
bash ./install.sh

Functionality:

Re-evaluates the quality of called SNPs (provided in VCF format). Returns:

• the reliability of a SNP (BOD score) based on the described geometric method

• per-nucleotide coverage of the reference around SNPs is returned either as:

  • a tab-delimited file (coverage for the range of +/- floor(1.5 * read length) around the SNP, tab-separated file, with blocks delimited by \t|\t ):

  • an SQLite3 database with coverage written as blob columns (a faster option). The database can be read with the provided Python ReadCoverage.py class and related scripts

• following coverage data is returned within QdrArray objects:

  • accounting for perfectly matching reads with 100% identity (HI) and loosely matching, between 90% and 100% identity (LO)
  • for forward and reverse strands

• three QdrArray objects with coverage profiles are returned:

  • for all reads in the range (totCov column in the SQLite database)
  • for reads covering only the locus proper (snpCov column)
  • location of centres of the reads covering the SNP locus (alnCtr column)

• the coverage data is written in a sampleX__coverage table with a composite key of (contig, pos), where contig is of TEXT type and pos (position) of INT type.

Test sample files:

Test sample files for running the program are in the folder testcase/. See bash script testcase/db_vshape_test.sh and testcase/tab_vshape_test.sh for example of vshape invocation. For conversion sqlite3 -> csv see testcase/dbtocsv.sh

Additional information:

A Python script (src/plot_coverage_sqlite.py) is provided to produce the plots of the coverage. An earlier R script (src/rscript.R) is outdated and is not compatible with the current version.

Contact:

If you have any questions/concerns please drop an email to:

fritz.sedlazeck@gmail.com

d.lituiev@gmail.com