Hi all,
I read lots of papers about SNP calling and the different implementations (GATK, SAMtools, SOAPsnp, etc) in the last time. Something I noticed was that in no paper run time performances where presented, neither in the papers introducing new SNP callers nor in surveys.
The only thing I came across where comments like "xy is comparably slow" (e.g., about SAMtools or GATK), but I cannot find exact numbers for run time performances anywhere.
Does anyone know why this is the case? Despite the comments I found, are SNP calling tools maybe that performant that run time performance is nothing to speak of?
Or even better, can anyone point me to any resource (papers, websites, forums, etc) where SNP calling tools have been compared to each other regarding run time performance or at least provide ANY data about run time performance?
Thank you,
CindyF
I read lots of papers about SNP calling and the different implementations (GATK, SAMtools, SOAPsnp, etc) in the last time. Something I noticed was that in no paper run time performances where presented, neither in the papers introducing new SNP callers nor in surveys.
The only thing I came across where comments like "xy is comparably slow" (e.g., about SAMtools or GATK), but I cannot find exact numbers for run time performances anywhere.
Does anyone know why this is the case? Despite the comments I found, are SNP calling tools maybe that performant that run time performance is nothing to speak of?
Or even better, can anyone point me to any resource (papers, websites, forums, etc) where SNP calling tools have been compared to each other regarding run time performance or at least provide ANY data about run time performance?
Thank you,
CindyF
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