I have used a VCF file that was produced by GATK for the -L option of DiagnoseTargets, but I get the alternative allele from the original VCF as the reference allele on the output vcf from Diagnose targets:
input VCF:
chr1 10425470 . G A 139.99 SNPBHF AC=1;AF=0.042;AN=24;BaseQRankSum=-5.862e+00;Clipp......
chr1 10425470 . A <DT> . PASS END=10425470;GC=1.00;IDP=805.00 FT:IDP:LL:ZL......
The GC content reflects the reference allele though.
Is this normal behaviour or a bug?
