gatk, ref and alt percentages .

Hello everyone,

I need some info regarding how to get percentage of REF and ALT nucleotide sequence in my data.

I am using gatk and currently not getting REF and ALT percentages .
the command i am using for the gatk vcf file is following

gatk –java-options “-Xmx8G” HaplotypeCaller -R /Users/sabeen/NGS/singleread/1/hg19.fa -I /Users/sabeen/NGS/singleread/1/reads-with-RG.bam -O /Users/sabeen/NGS/singleread/1/output_final.vcf

(how i need the info for for the refernce and alternative nucleotide in percentages as follows.)

Ref
G(52%) A(32%)

Alt

A(48%) T(68%)

Really appreciate some guidance .
Thanks.