integrate vcf files

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

vcf

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written 10.3 years ago by Bogdan

2 answers

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

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written 10.3 years ago by harold.smith.tarheel

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 ?

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written 10.3 years ago by Bogdan

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