Suggested Pipeline Configuration 5.2.7

Example Variant Calling Pipeline:

Application	Function	Somatic	Germline	Notes
forthcoming	indel realignment	yes	yes	This is slow. 2-3x slower than the whole Pisces step. You can skip it if you don't need the precision. Gets rid of a lot of false positives if the upstream aligner tends to make a lot of judgment errors.
Stitcher	stitches reads	yes	yes	reconciles pairs of reads into single consensus reads,reduces FP due to noise, reduces FN due to strand bias, only works with paired end sequencing
Pisces	variant calling	yes	yes	use -ThreadByChr for faster performance but greater memory hit. Use qsub on the cluster, works fine with UMIs or for catching variants < 0.01%, so long as the data quality supports this and Pisces is properly configured.
Q Score Recalibration	Downgrade Q score for poor samples	yes	no	Run before or after scylla. Somatic calling is quite sensitive to sample degradation, germline calling less so. Gets rid of a lot of false positives if the samples has a lot of FFPE or oxidative damage that otherwise would dominate the variant calls.
Scylla	long range phasing	yes	yes	Default configuration works well with somatic. Special germline settings: ploidy=diploid, crushvcf=true, dist=5;must load the same bam that pisces does. Ie, if Pisces acts on a stitched or re-aligned bam, then so should Scylla,Turn off upstream MNV calling by Pisces.