Hi all, as many posts on this topic are quite old I would like to know what are the current recommendations for the BAQ parameters (-B or -E or none at all)?
1) Do you use GATK indel realignment and base quality score recalibration together with BAQ calculation as in the WGS/WES workflow example on the samtools page? There is a paper from Guo, 2012, The effect of strand bias in Illumina short-read sequencing data, mentioning strand bias problems with this combination 2) What is the drawback of turning BAQ calculation off (with the -B option), the manual only mentions a reduction of false-positive SNPs? 3) What is the difference between BAQ recalculation (-E) and no parameter at all, both should calculate BAQ values? Any examples/recommendations from your current workflows are welcome. Thanks, Christian ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
