Search Results for "varscan"
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Showing 5 open source projects for "varscan"
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somatic.sh
script for somatic SNP and Indel calling
somatic.sh is a shell script to run varscan somatic for somatic variant-calling, and Annovar to annotate. It calls both SNPs and Indels. It also produces 2 MAF files compatible with MutSigCV. Now the script allows for multithreading. The script is updated according to new format. -
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exome-test
script for variant calling of Exome-Seq
...-ni option added. -vb option (-B in varscan) added exac03nontcga is added. An error about VARSCAN is corrected. Mutlithreading for dbsnp annotation, Haplotypecaller, Varscan and bamreadcount more efficient. UMI function is added. Allelic fraction is added. Better COSMIC and CLINVAR annotation. -
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...The script uses the files produced by exome_test.sh. An error is corrected. The script also produces MAF file that only includes variants detected by BOTH GATK and Varscan. A few errors are corrected.
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4
VarScan
Variant detection in next-generation sequencing data
Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB -
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5
MethylExtract
High-Quality methylation maps and SNV calling from BS-Seq experiments
...The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in SNP and genotype calling based on non-bisulfite treated reads.
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