Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • mpileup and homozygous snps

    Hi all,

    I'm new to SNP-calling with mpileup/bcftools. After my first analysis it seems to me, that I cannot properly call homozygous SNPs...

    whole command (samtools-0.1.16):
    samtools mpileup -uf my.fa my.bam | bcftools view -vcg -

    1. output of mpileup (here in pileup-format, looks homozygous to me -> G?!):
    chrX 2779570 A 41 GGGGGGGGGGGGGGgGgGGGGGGGGGgGGgGGGGgGGGGGg I<FHIIBEB?FIIIIEGGHIIIGHGDGIHDBIGIH=IIIH#

    2. output of bcftools (looks heterozygous to me):
    chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

    Can anyone tell me the reason for this behaviour?
    Thank you.
    Last edited by grievous; 06-19-2011, 10:46 AM.

  • #2
    Have you solved this problem? I also have this problem, and I'm very interested in the result.

    Originally posted by grievous View Post
    Hi all,

    I'm new to SNP-calling with mpileup/bcftools. After my first analysis it seems to me, that I cannot properly call homozygous SNPs...

    whole command (samtools-0.1.16):
    samtools mpileup -uf my.fa my.bam | bcftools view -vcg -

    1. output of mpileup (here in pileup-format, looks homozygous to me -> G?!):
    chrX 2779570 A 41 GGGGGGGGGGGGGGgGgGGGGGGGGGgGGgGGGGgGGGGGg I<FHIIBEB?FIIIIEGGHIIIGHGDGIHDBIGIH=IIIH#

    2. output of bcftools (looks heterozygous to me):
    chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

    Can anyone tell me the reason for this behaviour?
    Thank you.

    Comment


    • #3
      This is surely a heterozygos SNP site from A to G

      Comment


      • #4
        2. output of bcftools (looks heterozygous to me):
        chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

        I think this is heterozygous SNP, you can see this values 0/1:99

        Comment


        • #5
          Strange. One suggestion...try

          samtools mpileup -Buf my.fa my.bam | bcftools view -vcg
          The -B turns off BAQ recalculation..I've gotten strange results when it was on, which were repaired by turning it off.

          Comment


          • #6
            You could try a different SNP calling program like freebayes or gatk.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Exploring the Dynamics of the Tumor Microenvironment
              by seqadmin




              The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
              07-08-2024, 03:19 PM
            • seqadmin
              Exploring Human Diversity Through Large-Scale Omics
              by seqadmin


              In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
              06-25-2024, 06:43 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 07-19-2024, 07:20 AM
            0 responses
            32 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-16-2024, 05:49 AM
            0 responses
            43 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-15-2024, 06:53 AM
            0 responses
            53 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-10-2024, 07:30 AM
            0 responses
            43 views
            0 likes
            Last Post seqadmin  
            Working...
            X