VarScan

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VarScan Free Download is a command-line tool for identifying simple nucleotide polymorphisms (SNPs) and Indels in the human genome. VarScan Cracked Accounts makes many sequence alignment tools accessible via the command line. Among its features is a likelihood based algorithm that incorporates information about indels to account for the possibility that some small variants may be due to the deletion of a single nucleotide.
When scanning the human genome, VarScan Cracked Accounts includes multiple options for filtering, such as quality score, overlapping paired-end, allele frequency, and probe summarization. VarScan Product Key is a free tool.
(Java)
usage: java net.sf.varscan.VarScan [COMMAND] [OPTIONS]
The commands available can identify SNPs and Indels from a Sam Tools pileup file (pileup2snp and pileup2indel), along with SNPs and Indels from an mpileup file (mpileup2snp and mpileup2indel), as well as call consensus and variants from a pileup and mpileup file (pileup2cns and mpileup2cns).
Moreover, you can call germline or somatic variants from tumor-normal pileups (somatic), determine the relative tumor copy number from tumor-normal pileups (copynumber), get read counts for a list of variants from a pileup file (readcounts), filter SNPs by coverage, frequency, p-value and other criteria (filter), and filter somatic variants for clusters or Indels (somaticFilter).
Lastly, it’s possible to isolate germline, LOH or somatic calls from the output (processSomatic), call copy number changes from the somatic copy number output (copyCaller), compare two lists with positions or variants (compare), as well as restrict the pileup, SNPs or Indels to ROI positions (limit).
VarScan Description:

VarScan is a command-line tool for identifying simple nucleotide polymorphisms (SNPs) and Indels in the human genome. VarScan makes many sequence alignment tools accessible via the command line. Among its features is a likelihood based algorithm that incorporates information about indels to account for the possibility that some small variants may be due to the deletion of a single nucle

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COPYVALUE The number of times a genomic segment is read in a sample. The expected value is approximately 3 for coverage, 1 for tumor copy number.
COPYNUMBER The number of copies of a segment in a sample. The expected value is 1.
COPYFREQ The number of reads that contain the same genomic segment as the one in the segment list. The expected value is 1.
COPYVALUE_FREQ The average coverage per read across the segment in the sample. The expected value is 3 for coverage.
COPYNUMBER_FREQ The average tumor copy number across the segment in the sample. The expected value is 1.
GENDER The specific chromosome in the sample. The expected value is ‘-1’.
GENDER_FREQ The average copy number of the segment in the chromosome in the sample. The expected value is 1.
GENDER_TYPE The type of the segment. The expected value is ‘-1’.
GENDER_TYPE_FREQ The average copy number of the chromosome in the sample. The expected value is 1.
HOST Sample name.
HOST_FREQ Average coverage per read across the segment in the sample. The expected value is 3 for coverage.
INDELCHANNEL The chromosome in the sample. The expected value is ‘-1’.
INDELCHANNEL_FREQ The average copy number of the segment in the chromosome in the sample. The expected value is 1.
INDSITE The genomic location of the segment. The expected value is ‘-1’.
INDSITE_FREQ The average copy number of the segment in the sample. The expected value is 1.
INDSITE_TYPE The type of the segment. The expected value is ‘-1’.
INDSITE_TYPE_FREQ The average copy number of the chromosome in the sample. The expected value is 1.
LOHCHANNEL The chromosome in the sample. The expected value is ‘-1’.
LOHCHANNEL_FREQ The average copy number of the segment in the chromosome in the sample. The expected value is 1.
LOHTYPE The type of the segment. The expected value is ‘-1’.
LOHTYPE_FREQ The average copy number of the chromosome in the sample. The expected value is 1.
LOHVAR The genomic location of
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The project was originally developed for the SOLiD V2 SOLiD
technology, and has been thoroughly tested on both the Roche/454 and
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Note: For the latest version, please visit github ( or readme.

VarScan: Finds Variants in Sequencing Reads.
VarScan v2.3.4 is a command line tool for finding variants in sequencing data. It is designed to be used by scientists who need to annotate whole-exome sequencing or whole-genome sequencing data. VarScan will take your sequencing reads and use them to find all the variants in the exome or genome, including SNPs, indels, and short tandem repeats.

By the way, this tool is very useful for finding somatic variants from cancer sequencing data. It can separate SNPs, Indels, short tandem repeats and SNPs from each sample. And it can find somatic variants from your tumor-normal sample pair.

How does VarScan compare to other tools?
VarScan is designed to take sequencing reads, and find all the variants that the reads contain. Other existing tools that we know of are designed for producing SNP or Indel call files.

The advantage of VarScan is that it can tell you if the variant is in the coding region, as well as what allele it has. This information is more valuable than just calling the variant as “SNP” or “Indel.” If you want to know more about the variant, VarScan gives you the exact position of the variant in the reference genome, as well as all of the flanking sequence on either side of the variant.

VarScan supports 4 different technologies:

Next Generation Sequencing of DNA
The simplest thing to do is to run VarScan on a bunch of sequencing reads that you’ve downloaded from the internet. When you run VarScan, it will look at the sequence in the sequencing reads and search for the exact positions that the reads overlap.

Sequencing of DNA from individual samples
VarScan can look at DNA sequencing data from individual samples. The first step is to make sure that you can tell your data apart. If you’re using paired-end reads, you can make sure that the samples are sequenced from different pairs.

For example

What’s New In VarScan?

VarScan is a command-line utility for identifying simple nucleotide polymorphisms (SNPs) and Indels. It facilitates variant detection for next-generation data parallel sequencing of individual and pooled samples. The tool is free for non-commercial use.

SNPs are DNA sequence variants which usually occur in a population where a single nucleotide in the genome different than the shared sequence varies between the members of biological species or coupled chromosomes. Meanwhile, ‘Indel’ is a term in molecular biology used to find out when bases are added or removed from DNA.
Based on the data supplied for a single sample, this application detects and filters germline variants by taking into account the read counts, base quality, and allele frequency. Similarly for a tumor-normal pair, it compares the read counts between samples, in order to calculate the somatic status of each germline, somatic or LOH variant. It can merge and intersect two lists of variants.

The usage is java net.sf.varscan.VarScan [COMMAND] [OPTIONS]
The commands available can identify SNPs and Indels from a Sam Tools pileup file (pileup2snp and pileup2indel), along with SNPs and Indels from an mpileup file (mpileup2snp and mpileup2indel), as well as call consensus and variants from a pileup and mpileup file (pileup2cns and mpileup2cns).

Moreover, you can call germline or somatic variants from tumor-normal pileups (somatic), determine the relative tumor copy number from tumor-normal pileups (copynumber), get read counts for a list of variants from a pileup file (readcounts), filter SNPs by coverage, frequency, p-value and other criteria (filter), and filter somatic variants for clusters or Indels (somaticFilter).

Lastly, it’s possible to isolate germline, LOH or somatic calls from the output (processSomatic), call copy number changes from the somatic copy number output (copyCaller), compare two lists with positions or variants (compare), as well as restrict the pileup, SNPs or Indels to ROI positions (limit).

Comment to the author:
*Please use commas to separate your arguments when using the Command Line.
* The program will fail if you call it with any other than a single file as input.
* If your input file contains blank lines or lines without metadata, the program will fail and be sure to read the documentation before running the program.

The current distribution contains examples to explain what the program does.

Example 1:
The -W option is required to add a header to each variant for filtration later on. Also, the -D option is needed to specify the sample directory

System Requirements:

For performance and stability reasons, the image displayed in the Options Dialog will only be available to those products with an appropriate version number. If your product does not match this requirement, we regret that this option is not available for you. Please refer to the system requirements for more information.
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Tag: VarScan

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System Requirements: