Hello, I realize that bcftools som (self-organizing map) was used in the 1000 Genomes Project phase3 for filtering the variant calls made by samtools. There is very limited documentation out there about this functionality; it looks might still be experimental. Is this functionality ready to be used for production? If not, could you please suggest an alternative for filtering variants called by Samtools/BCFtools? 'VCFutils.pl varFilter' has been the filtering method.
For bcftools som, looks like one has to train it first using an annotation file of known variants (the annotations are like HWE, MP0 etc.). Do you know if there is a training set handy on GRCh38? Another question is whether samtools/bcftools is suitable for calling variants with exome data. I knew samtools/bcftools was used for low coverage calling in the 1000 Genomes Project. Wonder if it can be used for calling variants for exome data, separately from low coverage data. Calling low coverage plus exome data together might be a bad idea. Thanks for your kind help in advance. Holly ------------------------------------------------------------------------------ Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
