WGS data and looking for SNPs and Indels globally.
we found Indels and SNPs using PCR and also when we load the sequencing data on
IGV, we can see those events by eye (of course with low frequency). but when we used the following tools we can not detect them in the resulting VCF file:
lofreq , mutect, strelka and bcftool
do you know what could be the problem?