gatk, ref and alt percentages .
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.)
Really appreciate some guidance .
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