RELEASE NOTES FOR VARSCAN V2.3.6

29-July-2013

VarScan v2.3.6 includes these bug fixes:
-Corrected VCF output format for deletions, which had a bug
-For somatic, fixed a bug so that --strand-filter can be set to 0 or 1.
-Fixed an issue with mpileup2cns where it crashed at the strange SAMtools mpileup lines with 0x depth.
-Turned off a debugging message concerning indels ("failed with A+").
-Added VCF compatibility for the filtering commands

MORE VCF COMPATIBILITY
The following commands are now compatible with VCF files:
processSomatic
filter
somaticFilter

NEW FEATURE: TRIO CALLING
A method for trio calling is now available with the subcommand "trio". We have used it internally, but this is the first external release 
of the code, so I'd consider it a "beta" feature. Your feedback is welcome!

Usage:
java -jar VarScan.jar trio [fatherMotherChild.mpileup] [varScan.output] 

Your input file [fatherMotherChild.mpileup] should be a SAMtools mpileup file with father, mother, and child data, in that order. 

The [varScan.output] is a basename for your output VCFs. VCF is the only output format option.

If you provide piped input, you must use the --output-name parameter to specify a basename for output files.

Output:
Two VCFs, one for SNPs and one for indels, e.g. varScan.output.snp.vcf and varScan.output.indel.vcf

Methods:
This feature employs some special methodology to aid family studies:

1.) Detection of de novo mutations. The underlying assumptions are that the parents truly are the biological parents, and that true de novo mutations are rare. 
We define a de novo mutation as a variant present in the child but absent from both parents. Other differences, such as two homozygous-variant parents and a wild-type child, are classified as MIE (Mendelian Inheritance Error).
Candidate de novos (mother=0/0 father=0/0 child!=0/0) are re-called using a separate set of user-defined parameters (see usage) to detect under-sampled variants in either parent.

2.) Trio status. Other trio statuses (transmitted, untransmitted, or Mendelian inheritance errors) are represented in the STATUS info field. 

3.) MIE Checks. If apparent violations of Mendelian inheritance are observed, first VarScan attempts to re-call the trio with relaxed settings to obtain compatible genotypes. If this fails, the FILTER field will be mendelError.

Notes: 
-The --min-coverage parameter is set to 12 and applies to ALL three samples (otherwise the site won't be called). This prevents a lot of power-of-detection issues at low coverage. For even more conservative results, set --min-coverage to 20.

USE THE FILTER!
Note, if you use VarScan you should also employ the false-positive filter described in the VarScan 2 publication.
-For somatic mutations, filter with the Tumor BAM. For LOH and Germline, filter with the Normal BAM
-For de novo mutations (trio calling), filter with the child BAM.
See the fpfilter.pl and fpfilter-help.txt files here: https://sourceforge.net/projects/varscan/files/scripts/
The filter requires the bam-readcount utility: https://github.com/genome/bam-readcount

LICENSE
VarScan 2 is licensed under the Non-Profit Open Software License 3.0 (NPOSL-3.0)

CITING VARSCAN
If you use VarScan, please note the version number and cite this publication along with the URL:

Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. 
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. 
Genome Res. 2012 Mar;22(3):568-76. doi: 10.1101/gr.129684.111. 
http://varscan.sourceforge.net


