I am struggling with identification of large insertion/deletion as well as variants calls. I have used the GATK for snps call s and realized that GATK tools identified up to 50bp(?) insertion/deletion as well as SNPs.
However I am wondering whether I could also detect the large size insertion/deletion from paired-end NGS data.
I know that insertion is much more difficult to detect .. And especially, insertions which are larger than the distance of paired ends reads could not be detected (impossible to detect).. Then, still can I detect the large size deletion ?
Is there any size limit for Indels we can detect ? In my case, my fragment size is 52bp ~ 546bp.. And median size is 216bp. In this case, how long Indel can I detect?? What kind of tool I have to use?