If I have a vcf file, and some variants have more than one alternative alleles, like:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
Chr_3.1 124358 . G GCCCC,GCC 32.2 . INDEL;IS=2,0.200000;DP=10;VDB=6.695005e-02;AF1=1;AC1=2;DP4=0,0,1,2;MQ=60;FQ=-40.5 GT:PL:DP:GQ 1/1:104,39,33,69,0,66:3:10
How can I know which one is adding vcf-consensus to the new reference?
Thanks in advance.