Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • question about the summary statistics

    Hi,

    I have samples that we have exome sequence. Threse have been aligned using BWA and variants called using GATK. I would like to calculate the summary statistics across all the individuals (not for each sample )( for example, the percentage of reads aligned , the mean target coverage etc). can this be done? If so how?

    Thanks,
    Kay

  • #2
    Two options

    Have you gotten your answer in other means, Kay?

    Otherwise, you can take a look at the following technique:

    Code:
    # Obtain depth of coverage for all target regions
    /path/to/samtools depth /path/to/.bam -b /path/to/.bed > coverage_depth.tsv
    # Enumerate the occuring coverage values
    cut -f3 coverage_depth.tsv | sort | uniq -c | sed 's/^[ \t]*//;s/[ \t]*$//' >coverage.tsv
    # Make bam file for on-target reads only
    /path/to/samtools view -b /path/to/.bam -L /path/to/.bed > ontarget.bam
    /path/to/samtools index /path/to/ontarget.bam
    #Retrieve number of reads mapped and unmapped in ontarget files
    /path/to/samtools idxstats ontarget.bam > stats_ontarget.idxstats
    #Retrieve number of reads mapped and unmapped in original
    /path/to/samtools idxstats /path/to/.bam  > stats_overall.idxstats
    You should also check the enrichment technique offered by pfrommolt in this post:
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc
    "Though it may seem that all's been said and done, originality still lives on" - some unoriginal guy who had nothing better to write as his signature

    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
    10 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
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X