Insert your VCFs in a sqlite database.

vcf2sqlite is C++ tool that is part of my Variation Toolkit.
It inserts a "Variant Call Format document" (VCF) into a sqlite3 database.

Download

Download the sources from Google-Code using subversion:....

svn checkout http://variationtoolkit.googlecode.com/svn/trunk/ variationtoolkit-read-only

... or update the sources of an existing installation...

cd variationtoolkit
svn update

... and edit the variationtoolkit/congig.mk file.

Dependencies

http://www.sqlite.org/ : libraries and headers for sqlite3.

Compilation

Define "SQLITE_LIB" and "SQLITE_CFLAGS" in config.mk (see HowToInstall )

$ cd variationtoolkit/src/
$ make ../bin/vcf2sqlite 

if ! [ -z "$(SQLITE_LIB)" ] ;then g++ -o ../bin/vcf2sqlite vcf2sqlite.cpp xsqlite.cpp application.o -O3 -Wall -lz   ; else g++ -o ../bin/vcf2sqlite vcf2sqlite.cpp  -DNOSQLITE -O3 -Wall  ; fi

Usage

vcf2sqlite -f database.sqlite (file1.vcf file2... | stdin )

Options

• -f (file) sqlite3 database (REQUIRED).

Schema

Example:

$ vcf2sqlite -f db.sqlite file.vcf
$ sqlite3 -line db.sqlite  "select * from VCFCALL LIMIT 4"

       id = 1
   nIndex = 0
vcfrow_id = 1
sample_id = 1
     prop = GT
    value = 1/1

       id = 2
   nIndex = 1
vcfrow_id = 1
sample_id = 1
     prop = PL
    value = 46,6,0

       id = 3
   nIndex = 2
vcfrow_id = 1
sample_id = 1
     prop = GQ
    value = 10

       id = 4
   nIndex = 0
vcfrow_id = 2
sample_id = 1
     prop = GT
    value = 1/1

$ sqlite3 -column -header  db.sqlite \
   "select SAMPLE.name,VCFCALL.value,count(*) from VCFCALL,SAMPLE where SAMPLE.id=VCFCALL.sample_id and prop='GT' group by SAMPLE.id,VCFCALL.value"

name         value       count(*)  
-----------  ----------  ----------
rmdup_1.bam  0/1         545       
rmdup_1.bam  1/1         429       
rmdup_2.bam  0/1         625       
rmdup_2.bam  1/1         349       
rmdup_3.bam  0/1         595       
rmdup_3.bam  1/1         379       
rmdup_4.bam  0/1         548       
rmdup_4.bam  1/1         426       
rmdup_5.bam  0/1         564       
rmdup_5.bam  1/1         410       
rmdup_6.bam  0/1         724       
rmdup_6.bam  1/1         250

That's it
Pierre