Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Questions about VarScan

    Hi all. I'm a student working to identify tumor-specific mutations.

    Recently I've came up to VarScan and SomaticSniper.

    There are some confusions about using VarScan, and I see that the documentation is somewhat lacking in catching up its own versions, so I ask this question here !

    I'm using VarScan.v2.2.8.jar somatic when doing my analyses.

    1. When What is the "germline p-value" exactly?
    1.1. I see that --somatic-p-value sets a p-value to statistically test (Fisher's exact test) whether "normal variant allele frequency of one locus" is the same as "tumor variant allele frequency of one locus".

    ( Many thanks about the discussion here (it really was a great help! ):
    http://seqanswers.com/forums/showthr...hlight=varscan )

    So for example, I thought such contingency table could be made (I drew it crudely because I could not put in spaces instead of hyphens and underscores; ugly, isn't it?):
    ------------Normal--Tumor
    Reference___10______2
    1 Variant_____2______8 --> Fisher's exact p-value calculated.

    ...where the counts are reads mapped to the locus.

    1.2. However, how can a "germline p-value" be calculated? D. Koboldt (the developer) himself explained that this germline p-value is "the null hypothesis is that the sample is homozygous-reference; under this hypothesis, all reads should support the reference base", which I do not understand exactly. I ask for a comment about this matter.


    2. Can VarScan emit output in VCF (variant call format)?
    It is written that now VarScan supports output to be in VCF, as written on the main web page as "VarScan v2.2.8 released with new somatic calling features: Tumor-normal mpileup compatibility and VCF 4.1 output option." (http://varscan.sourceforge.net/index.html)
    However, all I can find inside the documentation (or I'm doing something wrong) is about v2.2, not v2.2.8.


    I really hope somebody could give me a warm hand.

    Have a great day!!
    Last edited by alexbmp; 02-12-2012, 11:13 PM. Reason: To draw a table and add details

  • #2
    Hello,

    The germline P-value in VarScan output is computed when a site has been classified as Germline (the same in both normal and tumor). In this situation, the read counts from normal and tumor are combined into a total number for each allele (reference and variant). This is compared via Fisher's Exact Test to the null hypothesis, a wild-type position, at which all reads should reflect the reference allele.

    The VCF 4.1 output option is available with VarScan 2.2.8 and above. However, it is currently only enabled for multi-sample calling functions mpileup2snp, mpileup2indel, and mpileup2cns. We are working on making VCF output an option for somatic mutation calling for the next release.

    Comment


    • #3
      Hi dkoboldt,
      I've just started using VarScan (v2.2.11) and so far am very happy with what it can do. I am formatting my output from mpilup2snp and mpileup2indel as VCF, but, for me at least, the output is in version 4.0 (see header information below), not 4.1 as stated above. Is there another option distinct from setting "--output-vcf 1" to set it to version 4.1?

      ##fileformat=VCFv4.0
      ##source=VarScan2
      ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
      ##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
      ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
      ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
      ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">

      Comment


      • #4
        Hello,

        We've just released VarScan v2.3.1 with better VCF compatibility; it should create VCF4.1 output. If it does not, please let me know!

        Yours,

        Dan Koboldt

        Comment


        • #5
          Hi Dan,
          thanks very much for the announcement, and the new format seems to be working great!
          Gordon

          Comment


          • #6
            Hi,

            Is it possible to get vcf output using somatic mutation calling? If yes what should be the option in the command line?

            Comment


            • #7
              Originally posted by FrankiB View Post
              Hi,

              Is it possible to get vcf output using somatic mutation calling? If yes what should be the option in the command line?
              Same as for germline:

              --output-vcf 1

              Comment


              • #8
                Yes I see. Thank you very much

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  Strategies for Sequencing Challenging Samples
                  by seqadmin


                  Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                  03-22-2024, 06:39 AM
                • seqadmin
                  Techniques and Challenges in Conservation Genomics
                  by seqadmin



                  The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                  Avian Conservation
                  Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                  03-08-2024, 10:41 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, Yesterday, 06:37 PM
                0 responses
                10 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, Yesterday, 06:07 PM
                0 responses
                9 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-22-2024, 10:03 AM
                0 responses
                51 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-21-2024, 07:32 AM
                0 responses
                67 views
                0 likes
                Last Post seqadmin  
                Working...
                X