Dear everyone,
Recently I was analyzing some NGS data and genome polymorphysm. Though Pindel, I got the insertions and deletions of NGS against Reference genome. After Pindel2vcf the vcf format files were available. Here is my question: What dose the genetype ("0/0", "0/1" or "1/1") in the vcf file represent separately?
For example,
chr10_irgsp5 2279161 . CA C . PASS END=2279162;HOMLEN=9;HOMSEQ=AAAAAAAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:3,3 0/0:0,0
chr10_irgsp5 2313030 . CA C . PASS END=2313031;HOMLEN=10;HOMSEQ=AAAAAAAAAA;SVLEN=-1;SVTYPE=DEL GT:AD 0/0:1,2 0/0:2,2
chr10_irgsp5 2588340 . GTA G . PASS END=2588342;HOMLEN=3;HOMSEQ=TAT;SVLEN=-2;SVTYPE=DEL GT:AD 0/0:0,1 0/1:8,8
Thanks very much!
Yang
Good call - I was about to clarify that is what the genotype means in general, but I am actually a bit confused in this specific case: I don't know what pindel would give 0/0 indel calls.
Nevertheless, you can confirm if the indel is heterozygous (0/1) or homozygous (1/1) by checking the alignment (in addition to checking the reliability of the call)