Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • mpileup and pileup results

    Hi everyone.

    1. I tried to call the snps using both mpileup and pileup.
    There is more differences in snps calling numbers.
    I found that mpileup give me less snps compared too pileup which produce lots of snps calling.
    eg pileup = about 10 K snps while mpileup = about 800 snps

    i run using this command
    samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf

    is using mpileup is more thorough compared to pileup?

    btw, i call the snps from rice data.

    2. can anyone here explain how can i make use the genotype data that present in vcf 'FORMAT' ? I read already in the documentation but not really understand.

    Thanks all!

  • #2
    According to the documentation from Samtools pileup is now depreciated. Use mpileup.

    Apparently the algorithm is more complex, takes into account local realignment of reads around putative SNP positions and also can modify base qualities around these positions. See the part on BAQ in the mpileup docs.
    Probably mpileup is reducing the number of false positives here, but have a look at some of the data. I'm sure you'll see some patterns emerging.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      The Impact of AI in Genomic Medicine
      by seqadmin



      Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
      02-26-2024, 02:07 PM
    • seqadmin
      Multiomics Techniques Advancing Disease Research
      by seqadmin


      New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

      A major leap in the field has
      ...
      02-08-2024, 06:33 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 02-28-2024, 06:12 AM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-23-2024, 04:11 PM
    0 responses
    70 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-21-2024, 08:52 AM
    0 responses
    77 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-20-2024, 08:57 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X