Question: How to integrate custom variant callers for consensus genotyping using CGES?
gravatar for lakhujanivijay
25 days ago by
lakhujanivijay4.7k wrote:

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

Can someone suggest alternative ways for consensus genotyping ?

ADD COMMENTlink modified 24 days ago • written 25 days ago by lakhujanivijay4.7k

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.

ADD REPLYlink modified 24 days ago by lakhujanivijay4.7k • written 25 days ago by gb1.5k

gb I did not get you.

ADD REPLYlink written 23 days ago by lakhujanivijay4.7k
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