Indel and non synonymous coding variant detection in variant calling

Question

[genomics_buddy]

Dear all,

I am having a basic doubt about getting or predicting the INDELs and non synonymous coding variant in my VCF file. I am currently using BWA MEM, freebayes and snpEff tools for Variant calling and annotation. In the VCF file, i am not getting INDELs and non synonymous coding variant. I have tried with BWA MEM, samtools/mpileup and snpEff too. Still, I can't able to get the Indels in my VCF.

So, how do i can get Indel's and non synonymous coding variant details in which pipeline model. My data is from fungi samples, illumina paired-end.

Please help me to understand from where or which step i need to modify to get the details.

[Pierre Lindenbaum]

show us the commands please.