I have analysed 100 WGS samples and resulting VCF is high quality. However, some metrics in fastQC analysis almost always shows "FAIL", e.g. "per base sequence content" or "Per sequence GC content". Should these samples be excluded?
Most likely answer is no. For excluding the samples you will want to have some other solid evidence than FastQC category "FAIL".
There are several informative blog posts by authors of FastQC that I will direct you to. These should be useful in addressing points above: https://sequencing.qcfail.com/software/fastqc/
"FAIL"ing in one or more FastQC category is not unusual since the limits that are tested by default are for normal genomic sequencing. Many experiment will fail certain categories because of the context of experiment.
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