integrate vcf files

Question

[Bogdan]

Dear all, any suggestions regarding a package that integrates vcf files that are generated by various callers (eg Haplotype Caller, or Platypus), or somatic mutation callers (Mutect, Strelka, Varscan, Virmid etc ;) ? thanks !

bogdan

Answer 1

[harold.smith.tarheel]

Depending upon your definition of "integrate", BEDTOOLS, VCFTOOLS, or VCFLIB may work.

Answer 2

[Bogdan]

Thanks Harold. Please could you guys advise, if a VCF file does not have some fileds we are interested like like DR4 field, or SB (strand bias), what program could we use to add the missing fields ?