Structure Variation

[lunky-zao]

when I use a vcf with structure variation, It's warning skip Indel site, there are total skip Indel sites number is : 618346，after filter Remain SNP Number : 0. Does it mean that VCF files with structural variations cannot be used with this software?

[hewm2008]

yes.
A ：The soft will skip non bi-allelic(Singleton/ThreeMulti allelic) site and indel site (For bi-allelic indel, you can modify the "REF ALT" to only one base. see the Perl script at the end of this conversation

I provide a script here that can change bi-allelic indel to SNP, which can be reserved for calculation
BGI-shenzhen/LDBlockShow#7