Compare Vcf Files

Question

[win]

HI all, I was wondering if someone could help. What would be the best way to compare two VCF files? I was thinking of using BED tools but not sure if there is anything more advanced out there which can output statistics as well.

thanks in advance.

[SES]

There is a program called vcf-compare in vcftools for comparing files. That's probably a good start, though you'll have to be more specific if that is not exactly what you want (vcf-stats may also be of interest).

Answer 1

[Ashutosh Pandey]

Try vcftools. You will have to use tabix and bgzip that comes with tabix. These tools are basically for compressing and indexing the vcf file. It has to be done beofre using vcf tools.

Answer 2

[Pierre Lindenbaum]

I wrote a tool named vcf2sqlite: it put one ore more VCFs into a local sqlite3 database. The schema is simple and you can query the database using some simple SQL statements.

$ 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