Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • mpileup to STRUCTURE

    Hi all,
    Thought I would see if anyone has a different (better!) pipeline for collecting a set of SNPs from many bam files for use with STRUCTURE or other population genetic software. The end goal is to have a matrix with SNPs as rows and samples in column.

    Ex.
    x y z
    Site 1 T T G
    Site 2 G A C
    Site 3 A G G


    1. Create mpileup file
    2. Call SNPs (with your favorite software) for each sample
    3. Create merged SNP list, with the end of goal of having each position where there is a SNP in at least one sample
    4. Create consensus fasta file from mpileup for each sample
    5. Extract consensus nucleotide from each position (#3) from consensus fasta (#4)
    6. Merge files

    One problem is that some SNP sites found in particular samples may not pass quality filters in other samples. I would love to hear of other pipelines.

    Thanks!

  • #2
    Have you tried just sending the mpileup to bamtools call?
    samtools mpileup -gu -t DP -f ref.fasta -b bam_file_list.txt| bcftools call -cv - > genotypes.vcf
    You'll need to sort the bam files, with samtools sort for instance

    or the equivalent from freebayes
    freebayes -f $ref_fasta_file bam_string > vcf_name
    You'll need to "read group" the bams with bamaddrg -b bamfile and then index with bamtools index.

    Either of these should be filtered with vcftools or vcflib to keep the SNPs with a certain presence in the population, using calls of a certain depth for each sample, etc.
    Last edited by SNPsaurus; 08-11-2015, 07:30 PM.
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

    Comment


    • #3
      Thanks for these suggestions. I actually haven't explored bcftools or freebayes so should have a busy few days

      I will post an update once I come to a satisfactory solution.

      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
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      10 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
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X