problem with SNPs and Indels detectiong useng WGS data

we have 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?



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