Hi everybody,
I have a general question regarding variant calling using GATK. My question is maybe naive (or stupid) since I am new to NGS analysis...
I am half-way through my analysis using the best practices and for a lot of command lines that I used so far, I had to put references for known indels and snp (i.e dbsnp). So are the variants (or mutations) that will be found in my different libraries will be considered as technical mutations or as new variants if they do not correspond to known indels or snps?
I have a general question regarding variant calling using GATK. My question is maybe naive (or stupid) since I am new to NGS analysis...
I am half-way through my analysis using the best practices and for a lot of command lines that I used so far, I had to put references for known indels and snp (i.e dbsnp). So are the variants (or mutations) that will be found in my different libraries will be considered as technical mutations or as new variants if they do not correspond to known indels or snps?
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