ssf

[swvanderlaan]

I used the ssf option but for the INDELs I still get I and D as alleles. How do I fix this to have full alleles as per described in Figure 2 of https://www.biorxiv.org/content/10.1101/2022.07.15.500230v4.full.pdf?

[Cloufield]

Hi,
for some software, INDELs are represented as I and D for simplicity. However, once converted, the allele information is lost. gwaslab is not able to recover the exact allele information for now (for INDELs it is hard to obtain the alternative allele from a common reference file because indels often has multiple similar alleles like AG/AGG/AGGG). If the SNPID is in the format of 1_12345678_A_ACGT, it is still fixable, otherwise, you may need to check the source to obtain the allele information.