Miscellaneous tools for exome-seq: annotating SNP, counting molecules on start, etc.
To see the list of executable scripts run
$java -jar exome-tools.jar
To execute specific script run
$java -cp exome-tools.jar script_name
- MolCountExome and MolCountSNP ================================
Estimates the number of initial molecules using the number of read (pairs) with unique mapping offsets aka distinct reads. Those estimates are used to calculate 'molecular coverage' of exome-sequencing data and individual SNPs.
Usage:
$groovy MolCountExome input(sam or bam) exome_ref(refseq format) output [read length, default = 100]
$groovy MolCountSNP input(sam or bam) varinats(VCF format) output [read length, default = 100]
Note:
Exome table should have the following columns (for whole exome just download RefSeq genes UCSC GB table):
name chrom strand txStart txEnd cdsStart cdsEnd exonStarts exonEnds name2
- VcfAnnot and MutectAnnot ===========================
These scripts perform a comprehensive annotation of VCF and MuTect format entries:
- Search for matching dbSNP and COMSIC entries
- Search for parent transcript and segment (exon, intron or UTR)
- Translate mutation-related codons, find missense mutations and frameshift indels
Usage:
$VcfAnnot.groovy [options] file1.vcf[,file2.vcf,...]|folder/with/vcfs [path to folder with refGene, COSMIC and dbSNP data if not in script dir]
$MutectAnnot.groovy [options] mutect_output1[,mutect_output2,...] [path to folder with refGene, COSMIC and dbSNP data if not in script dir]
Note:
A bundle (134 Mb) with annotations should be downloaded from https://www.dropbox.com/s/q42rm9cdns9o5fx/vcf_annot_bundle.zip
It should be either placed in script parent directory or specified during execution