How to integrate custom variant callers for consensus genotyping using CGES?

Question

[lakhujanivijay]

Hi All

I am interested in calling consensus genotype for few germline samples using BAM files as initial inputs. The CGES (Consensus Genotyper for Exome Sequencing) paper describes a workflow where they have integrated 4 different variant callers - GATK, samtools, FreeBayes and Atlas-SNP-2.

While the approach seems good, I am wondering how to integrate "my favourite" variant callers in case if I don't want to use any one of the 4 that they have integrated. While the authors say that the method can accept variants from any algorithm, I am wondering how could that be achieved?

I am looking at the following link for executing CGES and it appears as if the program accepts VCF files (from any caller?) and that means first the usetr is supposed to get the VCF file from their own pipeline

https://github.com/v-a-s-a/galaxy.consensus

Can someone suggest alternative ways for consensus genotyping ?

[gb]

I am wondering how could that be achieved?

Because a vcf file is a text based file in a specific format, if it looks different it is not a vcf file anymore.

[lakhujanivijay]

gb I did not get you.