SV analysis and Report page overview
This pipeline assess structural variation throughout the genome using the BAM file(s) output by our Alignment/QC workflow, and provides an interactive visualization to browse potential SVs.
Report
-an interactive circos plot for visualizing SV calls
Output Files
Manta
manta/manta_analysis/results/variants/candidateSV.vcf.gz
-raw, long-range raw SVs detected by manta in compressed VCF format
manta/manta_analysis/results/variants/candidateSmallIndels.vcf.gz
-raw, short variants detected by manta in compressed VCF format
manta/manta_analysis/results/variants/diploidSV.vcf.gz
-raw, variants detected by manta in diploid mode, in compressed VCF format
manta/manta_analysis/results/variants/somaticSV.vcf.gz
-raw, variants detected by manta in somatic mode, in compressed VCF format