vc

Type Members

1. class FilterFreeBayesCalls extends ProcessTask with Configuration with FixedResources

   

   Applies various filters and ensures proper VCF formatting for variants produced by FreeBayes.

   Applies various filters and ensures proper VCF formatting for variants produced by FreeBayes.

   This application of tools follows the procedure in bcbio's use of FreeBayes: https://github.com/chapmanb/bcbio-nextgen/blob/master/bcbio/variation/freebayes.py Briefly, does the following in order: - fix ambiguous (IUPAC) reference base calls - remove alternate alleles that are not called in any sample - split MNP variants into multiple records - updates AC and NS - sort records using a fixed length window - standardizes the representation of variants using parsimony and left-alignment relative to the reference genome* - remove both duplicate and reference alternate alleles

   * See: http://genome.sph.umich.edu/wiki/Variant_Normalization

   * Tool Requirements: - vcflib (https://github.com/vcflib/vcflib - vt (https://github.com/atks/vt) - bcftools (https://samtools.github.io/bcftools/) - bgzip (https://github.com/samtools/htslib)

   You can set the path to the various scripts and executables within the configuration, or make sure they are on your PATH.

2. abstract class FreeBayes extends Task with Configuration with VariableResources

   

   Task for running FreeBayes, based on: https://github.com/chapmanb/bcbio-nextgen/blob/master/bcbio/variation/freebayes.py Does no pre-filtering for regions with high depth, but uses the --max-coverage option instead.

   Task for running FreeBayes, based on: https://github.com/chapmanb/bcbio-nextgen/blob/master/bcbio/variation/freebayes.py Does no pre-filtering for regions with high depth, but uses the --max-coverage option instead. Furthermore, no post-filtering of the calls are performed; see FilterFreeBayesCalls for applying post-calling filters.

   regionSize will only be used if no interval list is given.

   Tool Requirements: - freebayes (https://github.com/ekg/freebayes) - vcflib (https://github.com/vcflib/vcflib - bgzip (https://github.com/samtools/htslib) - parallel (http://www.gnu.org/software/parallel)

   Other Requirements - reference FASTA must have an FAI

   You can set the path to the various scripts and executables within the configuration, or make sure they are on your PATH.

   Please note that if the output VCF is a bgzip'ed VCF (vcf.gz) no index will be generated.

3. class FreeBayesGermline extends FreeBayes

   

   Performs Germline variant calling using FreeBayes according the the BCBIO best Practices

4. class FreeBayesSomatic extends FreeBayes

   

   Performs Somatic (Tumor/Normal) variant calling using FreeBayes according the the BCBIO best Practices

5. class Strelka extends Pipeline with Configuration with LazyLogging

   

   Runs the Strelka somatic variant caller from Illumina, cleans up after it and merges the results into a single VCF for downstream analysis.

6. class Varscan2Somatic extends ProcessTask with JarTask with FixedResources with Configuration

   

   Task for running VarScan2's somatic calling from pileup.