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They give you a pipeline on the website as well as the command line options. It should be just as easy as using samtools in order to call snps, am I right or am I wrong? Why or why not?
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mate check out the youtube videos on the GATK package .. its not as simple as just using samtools to call out snps because INDELs and systematic biases affect the calls ... samtools does not adjust for these..... spend the time and learn the GATK package, its well worth it -
The GATK is very picky about the formatting of its input files making it much more difficult to use the the samtools pipeline. The formatting is important though because the pipeline generally makes use of all available relevant information making it more sensitive than samtools.Comment
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