Merged calls (without assembly) have only homozygous ALT genotype and inheritance analysis.

[npatel22526]

Hello,

It seems to be great tool for merging SV calls from multiple tools. I did a quick run with provided script "run_test.sh" as well as with our data from "CNVnator", "Lumpy" and "Manta". In both cases when I looked at the output file it contains only homozygous ALT allele in genotype filed (i.e. 1/1). How should the GT field be interpreted ? Is there any flag that identifies whether call is heterozygous or homozygous alt.

Also, we are in lab interested in analyzing de novo SVs, is there a functionality that looks at genotype in multiple sample ? On that note, How metaSV treats multi sample VCF input, it is not giving any error when provided multi sample VCF from Manta or Lumpy ?

Thanks.

Best, Nick