gatk, ref and alt percentages .

Question

[Sabeen]

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 reference and alternative nucleotide in percentages as follows.)

Ref
G(52%)    A(32%)

Alt
A(48%)  T(68%)

Really appreciate some guidance .

Thanks.

[Guyssel]

Bonjour a tous, j'ai le même problème j'aimerai avoir Le pourcentage des ref et alt dans un fichier VCF de la forme :

#CHROM  POS ID  REF     ALT          QUAL
  Chr1               1000       .        A(20%)    G(80%)      7.30814

Bien Merci. je suis nouveau dans ce domaine.

[Pierre Lindenbaum]

This is an english forum. Merci.

[Guyssel]

please excuse me if I expressed myself in French

[Pierre Lindenbaum]

have a look at the FORMAT/AD in the genotypes.