Merging SNPs and indels VCF from strelka for ANNOVAR annotation

[lbeltrame]

Hello,

as part of my analysis workflow I'm using Strelka to compare sample pairs, and this results in two files, one for SNPs and one for Indels. For the purpose of annotation (and to show them to the rest of the laboratory) I would like to merge them in a single VCF and then annotate the results with ANNOVAR.

I know the GATK's CombineVariants can do the job, but I'm phasing out GATK usage unless absolutely required, and it feels way too "heavy" to use it just to merge two VCFs.

I looked at vcf-merge from vcftools, but apparently it doubles the VCF header when merging the two files (it keeps information from both, even if identical), and ANNOVAR can't cope with that (it will not convert the results to its own format).

For reference, what I used was:

vcf-merge passed.somatic.indels.vcf.gz passed.somatic.snvs.gz > comparisoname.vcf

Where both files have been already compressed and indexed with tabix.
If I use vcf-concat, the resulting file is readable by ANNOVAR, but I don't think I'm doing the right thing (as I'm just pushing things on top of each other).

Any suggestions I could use to merge these files?