What's new in VarScan 2.4.6
Mar 28, 2023
- VarScan v2.4.6 is the latest release and contains key improvements/fixing to the mpileup2somatic functionality introduced in v2.4.5.
New in VarScan 2.4.2 (Oct 7, 2020)
- The primary changes are minor bugfixes for user-reported issues:
- Better handling of mal-formed mpileup lines in VarScan copynumber
- Addressing missing segregation STATUS codes in VarScan trio and the addition of a new code (0) for "Unknown")
- Addressing a VCF format issue for somatic mutation calling, in which multi-allelic sites (classified as "UNKNOWN") were reported
- in non-standard VCF format (with forward slashes in the ALT column). VarScan 2 somatic should now report multiple variant alleles
- using the ALT1,ALT2 format and the genotype fields for normal and tumor samples should reflect the appropriate variant allele.
New in VarScan 2.3.8 (May 1, 2015)
- VarScan v2.3.8 now incorporates false-positive filtering! This works for single-sample variant calls
- or somatic/LOH/germline calls from the somatic command. Both native VarScan output format and VCF
- format variant files are supported. SNVs and indels are both supported.
- This new command replaces the functionality of the fpfilter.pl accessory script.
New in VarScan 2.3.7 (Jul 16, 2014)
- Fixed the issue of zero-depth lines in single-sample pileups for VarScan copynumber
- Fixed a similar issue causing inconsistent column output for multi-sample mpileups in VarScan mpileup2*
- Multi-sample VCFs generated with VarScan v2.3.6 and earlier might be missing sample columns.
New in VarScan 2.3.6 (Jul 30, 2013)
- 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!
New in VarScan 2.3.5 (Mar 21, 2013)
- Corrected VCF output format for mpileup2snp/mpileup2indel/mpileup2cns, particularly for indels
- Corrected a bug that was causing non-variant or different-variant lines to be output in mpileup2snp/mpileup2indel
- Addressed a bug that incorrectly counted reads at positions where no consensus call was made (CNS="N"),
- which sometimes producing reference-supporting read counts (reads1) of less than 0.
- Corrected a bug that was causing incorrect GC content calculations in the copynumber command
- Removed the warning about invalid mpileup for sites with read depth=0.
New in VarScan 2.3.4 (Jan 31, 2013)
- A correction to the way that genotype quality (GQ) is calculated in VCF output. It had been 0 - log10(p_value), but the correct calculation is 0 - 10 * log10(p_value)
- Changes to VCF output, particularly for indels, to meet VCF specification standards
- A new option to provide a file of sample names when calling multiple samples using mpileup files (--vcf-sample-list)
New in VarScan 2.3.3 (Nov 9, 2012)
- A maximum indel size of 99 bp was adjusted to allow indels up to 999 bp
- Locale-parsing errors with copyCaller (floating-point numbers represented with commas, e.g. in Europe) weren't fully fixed in v2.3.2. This has been corrected.
- GC content values over 100 were reported by some users; the GC-counting logic issue behind this has been fixed.
New in VarScan 2.3.1 (Aug 10, 2012)
- Expanded VCF compatibility for filter, somaticFilter, and processSomatic commands
- Extended the optional VCF fields for mpileup2snp, mpileup2indel, and mpileup2cns output to include all VarScan fields
- Made it possible to provide a list of sample names for VCF output for mpileup2* commands.
- Expanded copyCaller functionality to filter by depth and output candidate homozygous deletions
- Fixed a bug in the indel-filtering functionality of the filter command
- Fixed European locale parsing errors in the copyCaller command