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  • Question on calling SNPs using samtools/bcftools

    Hi,

    I am using samtools/bcftools to call SNPs. I have a question on bcftools, I don't understand why this SNP is not called by bcftools. For example, this is the result of test.bcf file, which is created by:

    Code:
    samtools mpileup -ugf ref.fa seq.bam >test.bcf
    chr21 8588396 . T A,X 0 . DP=13;I16=1,9,0,3,378,14392,73,1809,600,36000,180,10800,93,1075,42,642 PL 27,0,57,190,199,232
    From PL value, P(D|TT)=10^(-2.7), P(D|TA)=0. So TA allele should be the most possible allele.

    But in the processed vcf using this command:

    Code:
    bcftools view -c test.bcf > test_count.vcf
    This SNP is:
    chr21 8588396 . T . 4.76 . DP=13;AF1=0.4995;CI95=0.5,0.5;DP4=1,9,0,3;MQ=60;PV4=1,5.9e-05,1,1 PL 27
    There is no alternative base information, but the AF1 is about 0.5, which means this is an heterozygous allele. And, if I use the following command, there is no SNP called at all.

    Code:
    bcftools view -vcg test.bcf > test_count.vcf
    Why the alternative base is not A??? Is there any option I can choose to call this SNP?

    BTW, I am using samtools version 0.1.10-6.

    Cheers,

    Jun

  • #2
    Originally posted by nkwuji View Post
    Hi,

    I am using samtools/bcftools to call SNPs. I have a question on bcftools, I don't understand why this SNP is not called by bcftools. For example, this is the result of test.bcf file, which is created by:

    Code:
    samtools mpileup -ugf ref.fa seq.bam >test.bcf


    From PL value, P(D|TT)=10^(-2.7), P(D|TA)=0. So TA allele should be the most possible allele.

    But in the processed vcf using this command:

    Code:
    bcftools view -c test.bcf > test_count.vcf
    This SNP is:


    There is no alternative base information, but the AF1 is about 0.5, which means this is an heterozygous allele. And, if I use the following command, there is no SNP called at all.

    Code:
    bcftools view -vcg test.bcf > test_count.vcf
    Why the alternative base is not A??? Is there any option I can choose to call this SNP?

    BTW, I am using samtools version 0.1.10-6.

    Cheers,

    Jun
    Still unsolved... waiting for an answer...

    Comment


    • #3
      you need to apply the prior

      Comment


      • #4
        Originally posted by lh3 View Post
        you need to apply the prior
        Hi, Lh3,

        Thx for your reply. Could you elaborate it? I find an option in bcttools view

        -P STR, type of prior: full, cond2, flat

        Do you mean this option? What are the differences between them?

        Cheers,
        Jun

        Comment


        • #5
          Originally posted by nkwuji View Post
          Hi, Lh3,

          Thx for your reply. Could you elaborate it? I find an option in bcttools view

          -P STR, type of prior: full, cond2, flat

          Do you mean this option? What are the differences between them?

          Cheers,
          Jun
          Hi, could someone please comment on this please? I'm also looking into the differences between the "prior" commands, and I haven't been able to find anything on the internet. Any information would be helpful.

          Thanks!
          Lisa

          Comment


          • #6
            Hi,

            Another request here for some more information with regards the 'prior' and snp calling options of bcftools. I've been trying to learn how to change the parameters of the snp calling but can't find much information on how to change the parameters in bcftools.

            I've also got a second related question about bcftools, the mpileup page says
            BCFtools does not properly handle multi-allelic variants. It only takes the strongest non-reference allele.
            Does anybody know how much of an issue this is? I'm expecting a number of my SNPs to be heterozygous with no allele match to the reference, will this issue prevent me seeing them?

            Thanks in advance for any answers,

            Craig

            Comment


            • #7
              Originally posted by lh3 View Post
              you need to apply the prior
              -- (minus minus)
              Homepage: Dan Bolser
              MetaBase the database of biological databases.

              Comment

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