Entering edit mode
6.5 years ago
hdtms
▴
20
After processing a Indel Vcf file using vcftools, I obtained the number of Deletions and Insertions. The thing is the number of Deletions is double compared to the number of Insertions. I know it usually is higher but I do not think it should be this high. I don't if it is because of the process I used, which was just using the Indel Length given by the Vcf. Or if I have to use a programm or another method of processing.
You should mention the technology used to generate the data and the steps that you have taken to process it.
Also provide some details on how you filtered the raw variants, as especially indels tend to accumulate in certain regions, such as low-complexity stretches and homopolymers.
The technology used to obtain the data was Ilumina, (steps were not performed by me, can get into detail). Samples came from different populations, it is expanded exome. To filter the Variants I used GATK best practices to obtein Vcf. Then used VcfTools