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  • mpileup-varscan

    Hi all,
    I have aligned illumina reads to the reference genome using bowtie and then created mpileup file using sam tools. I have used varscan to call variants (SNPS) using mpileup2snp with min coverage 20, min reads2 4, min avg qual 20 and p-value 0.1 settings.I would like to determine heterozygosity & homozygosity.

    I get output from the varscan for some of the contigs repeated more than once showing showing different p-values, var frequency , strand filter, sample homo & sam hetero. I have counted the snps for each contig which shows strand filter-Pass. But I am confused how can i get p-value, var freq for each contig (if it is repeated more than twice)

    Is there any way filter the result in varscan to get values for each unique contig?

  • #2
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


    Check this out. It won't answer your question precisely, but will give a better understanding of the parameters in varscan..
    Did you run the mpileup with the -B parameter? Because if you didn't VarScan is bound to give faulty results..

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    • #3
      mpileup2snp

      Thanks you..I will try mpileup with -B option..
      I also get different results when I tried mpileup2snp with VCF format turned on/off in the options.

      I get more number of SNPs predicted when I put VCF format output turned on and get lower number of SNPs when I turned off VCF format off. Do u you know why varscan shows different results?

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      • #4
        Nope.. My experience with VarScan is very limited. Sorry.

        Comment


        • #5
          Thanks a lot..now it is fixed.

          Now I get same no of SNPS predicted even when VCF option turned on/off in Varscan, when I create samtools mpileup creation with -B option.

          I hope this helps some one

          Comment


          • #6
            Bioman1,

            Thanks for your post, and glad you got it straightened out!

            ~Dan Koboldt

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