gngs.tools (groovy-ngs-utils API)

Class Summary
Class	Description
AlleleNumber	A utility class to contain some functionality for computing allele numbers / counts
CoveragePosition
CustomInfo
DeletionPlot	Authors: Simon Sadedin
Delfin	A simple exon-by-exon deletion finder
DownsampleFASTQ	A simple tool for downsampling paired end FASTQ to achieve lower coverage.
ExtractFASTQ	Extract reads as pairs from a sorted BAM and writes them out to standard output in interleaved format.
FASTQDedupeActor
FastQIdent	Find sequences not present in a raw fastq file
GapAnnotator	Annotates regions with gene, transcript, CDS overlap and distance information, as well as custom annotation to gene associations ("panels") and sub-panels (groups of genes within a panel)
GeneCovStats
Genotype	A simple tool that measures the status of predefined SNPs in a a BAM file, where SNPs are provided as a VCF file.
HeaderCat	A utility to concatenate files that may have headers which should only be included once at the top.
LCSHPlot
LiftOver	Simple tool that translates between genome coordinates with automatic download and caching of the chain files.
MeanCoverageEstimator	Estimates the mean coverage of a BAM file quickly through random sampling.
MergePartitionedVCFs	A tool to merge together multiple VCFs that contain variants from distinct regions but which may be interleaved between different VCFs
MultiCov	A command line tool to rapidly calculate per-base coverage across multiple BAM files with extended support for coverage normalisation and variability calculation.
Pairs	Extracts read pairs from BAM or CRAM files sorted in coordinate order.
PedTrio
ReadSpans
SampleCorrelationPlot	Computes pairwise SNP correlation for a set of input VCFs, outputting as a plot or a table in TSV format.
Sex	Estimates the sex of a sample from one or more VCF file and prints to the console.
ShearingKmerCounter	Tool to count the frequency of kmers at the start of each read in a BAM file.
SortFASTH10X	Utility to sort interleaved 10X FASTH format
SplitFASTQ10X	Utility to split paired end FASTQ and write it out in interleaved 10X format
SplitLiveFASTQ	Splits FASTQ in block-gzipped files which can be written live simultaneously while this tool is streaming them out.
Table
Toolbase9
TrimBarcode10X	Utility to filter 10X barcode off the R1 FASTQ
VCFMergeSource	Utility class for tracking state of a specific VCF in the merge process
VCFtoDB	Utility to import variants to SQLite database rows
VCFtoPed	Simple utility to extract sample id and sex from VCF file, and then write that information as a PED file.
VInfo
VariantInfo

AlleleNumber

A utility class to contain some functionality for computing allele numbers / counts

CoveragePosition

CustomInfo

DeletionPlot

Authors:: Simon Sadedin

Delfin

A simple exon-by-exon deletion finder

DownsampleFASTQ

A simple tool for downsampling paired end FASTQ to achieve lower coverage.

ExtractFASTQ

Extract reads as pairs from a sorted BAM and writes them out to standard output in interleaved format.

FASTQDedupeActor

FastQIdent

Find sequences not present in a raw fastq file

GapAnnotator

Annotates regions with gene, transcript, CDS overlap and distance information, as well as custom annotation to gene associations ("panels") and sub-panels (groups of genes within a panel)

GeneCovStats

Genotype

A simple tool that measures the status of predefined SNPs in a a BAM file, where SNPs are provided as a VCF file.

HeaderCat

A utility to concatenate files that may have headers which should only be included once at the top.

LCSHPlot

LiftOver

Simple tool that translates between genome coordinates with automatic download and caching of the chain files.

MeanCoverageEstimator

Estimates the mean coverage of a BAM file quickly through random sampling.

MergePartitionedVCFs

A tool to merge together multiple VCFs that contain variants from distinct regions but which may be interleaved between different VCFs

MultiCov

A command line tool to rapidly calculate per-base coverage across multiple BAM files with extended support for coverage normalisation and variability calculation.

Pairs

Extracts read pairs from BAM or CRAM files sorted in coordinate order.

PedTrio

ReadSpans

SampleCorrelationPlot

Computes pairwise SNP correlation for a set of input VCFs, outputting as a plot or a table in TSV format.

Sex

Estimates the sex of a sample from one or more VCF file and prints to the console.

ShearingKmerCounter

Tool to count the frequency of kmers at the start of each read in a BAM file.

SortFASTH10X

Utility to sort interleaved 10X FASTH format

SplitFASTQ10X

Utility to split paired end FASTQ and write it out in interleaved 10X format

SplitLiveFASTQ

Splits FASTQ in block-gzipped files which can be written live simultaneously while this tool is streaming them out.

Table

Toolbase9

TrimBarcode10X

Utility to filter 10X barcode off the R1 FASTQ

VCFMergeSource

Utility class for tracking state of a specific VCF in the merge process

VCFtoDB

Utility to import variants to SQLite database rows

VCFtoPed

Simple utility to extract sample id and sex from VCF file, and then write that information as a PED file.

VInfo

VariantInfo

Package gngs.tools

Package gngs.tools Description