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state-of-the-art methods to obtain SNVs from circulating tumor DNA?

What is the state-of-the-art to obtain SNVs from circulating tumor DNA after Illumina sequencing? This is, finding a list of nucleotide locations that show tumour SNVs filtered out of any germline ...
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Is it common to get different number of SNVs+Indels across samples from vcf files generated using GATK and DRAGEN (counts are higher for GATK)?

We have 2 vcf (Whole Exome Sequencing (WES) data; germline samples) files (e.g., vcf_1 and vcf_2). vcf_1 was generated (Ref. genome: hg38) using the GATK pipeline for 250 children and their parents ...
Apurba Shil's user avatar