Same pipeline for exome seq variant calling with different results

Question

[paumarc]

Hello

we have been running a pipeline using fastp, bwa-mem, and gatk with hard filtering to perform snp calling on exome seq data. Although the coverage statistics for fastq files is similar, we obtain a huge difference in the number of reads per snp. We wonder if it could be caused by hard filtering. Otherwise, could you suggest any idea of what can be going on?

Thanks in advanced.

[WouterDeCoster]

Although the coverage statistics for fastq files is similar, we obtain a huge difference in the number of reads per snp.

I think that adding a bit more details here would increase your chance of getting an answer.