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Scaffold end SNPs and artifact checks
Hi,
I have been reading this blogpost (http://pathogenomics.bham.ac.uk/blog...dle-the-truth/) about SNP calling artifacts.
It does not describe a set of artifact check methods one could do to ensure that a particular region is immune from artifacts. Does anybody have any suggestions?
It also says specifically "Alignment to ends of contigs in draft assemblies". Could somebody explain how this will affect the SNP calls? Will it increase or decrease homozygosity?
Are there any guidelines about how to trim "ends" of contigs in draft assemblies. How long is a end of a contig?
Thank you for all your helpful suggestions.
I have been reading this blogpost (http://pathogenomics.bham.ac.uk/blog...dle-the-truth/) about SNP calling artifacts.
It does not describe a set of artifact check methods one could do to ensure that a particular region is immune from artifacts. Does anybody have any suggestions?
It also says specifically "Alignment to ends of contigs in draft assemblies". Could somebody explain how this will affect the SNP calls? Will it increase or decrease homozygosity?
Are there any guidelines about how to trim "ends" of contigs in draft assemblies. How long is a end of a contig?
Thank you for all your helpful suggestions.