varscan copynumber output
varscan pipeline
somatic mutation calling
varscan tutorial
varscan github
varscan ploidyvarscan fpfilter
samtools mpileup

12 Dec 2013 Alternate Protocol 1 describes exome-based copy number calling for .. Visual manual review of the sequencing data in a viewer such as IGV25 Aug 2015 according to the manual's instructions, shown here: samtools mpileup -q 1 -f ref.fa normal.bam tumor.bam | java -jar VarScan.jar copynumber Somatic copy number alterations (CNAs) in tumor-normal exome data. will be displayed. For details on using VarScan, please see the User's Manual. Somatic Copy Number Alteration (CNA) Calling. Overview Recommended Workflow Commands Input Methods Output Filtering/Adjusting Results with Germline Variants · Somatic Mutations · Copy Number Variants · de novo and a statistical test based on the number of aligned reads supporting each allele. 2 Feb 2012 The VarScan 2 mutation and copy number alteration detection .. We thank Heather Schmidt and Joelle Veizer for extensive manual review of About/Wiki · Project Page · User's Manual · JavaDoc · Download Now Germline Variants · Somatic Mutations · Copy Number Variants · de novo Mutations (Trios) Older versions of SAMtools use the pileup command, which is no longer mpileup] copynumber [normal pileup] [tumor pileup] or [normal-tumor mpileup] Variant Filtering: filter [variants file] somaticFilter [mutations file] Utility Functions: segments.p(segs, ngrid=100, tol=1e-6, alpha=0.05, search.range=100, nperm=1000). also see reference manual for DNACopy page 13-14. About/Wiki · Project Page · User's Manual · JavaDoc · Download Now (SNVs/indels) and the copynumber command to call copy number alterations (CNAs). a lower variant allele frequency (conservatively, 0.50 / the number of samples),