Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Extracting base coverage and quality values from BAM files

    Experts,
    I am interested in extracting base coverage and quality values for non SNP reads from a BAM file?
    Thanks,
    -Uma

  • #2
    pileup in samtools may be what you need.

    Comment


    • #3
      Yes, pileup is the tool from samtools to display coverage / quality information
      --
      bioinfosm

      Comment


      • #4
        Thanks for the info.
        Here is what I have tried so far to view the file for a given sample:
        samtools view filename.bam chr:start-end

        For non SNP positions, I am getting the base coverage using the following command:
        samtools view filename.bam chr:start-end |wc -l

        Sometimes the actual position is missing when I grep it and ~50 bases around it are printed. My question is how can I trust the wc -l value for a position if that position itself is missing in the BAM file?
        Last edited by unagaswamy; 10-21-2010, 12:37 PM.

        Comment


        • #5
          Hi Experts,
          Can anyone tell me how to extract the base quality from the CQ field of the BAM file? I colleague of mine mentioned that every two ASCII character corresponds to the SOLiD color space. Do I take the average of every overlapping 2 or the max? Any input in this regard is gretaly appreciated!

          Comment


          • #6
            Originally posted by unagaswamy View Post
            Hi Experts,
            Can anyone tell me how to extract the base quality from the CQ field of the BAM file? I colleague of mine mentioned that every two ASCII character corresponds to the SOLiD color space. Do I take the average of every overlapping 2 or the max? Any input in this regard is gretaly appreciated!
            Is the base quality not already reported in the SAM record (it should be)? As to how to calculate the base qualities during alignment from color qualities, here is the formula MAQ/BWA/BFAST uses: https://sourceforge.net/apps/mediawi...apping_Quality.

            Comment


            • #7
              Hi nilshomer,
              Thanks for the reply. We are generating SAM record only for the SNP positions which does have the base quality. I am interested in the Non-SNP positions as well and hence I'm trying to calcuate the base quality for these positions from the BAM file.
              -Uma

              Comment


              • #8
                Hi All,
                I generated a raw pileup for all reference positions using the samtools. An exmaple record for a non-SNP position is below:
                chrY 11936864 G G 51 0 60 8 ,,.,,,.. "%`".B"`

                This base has a coverage of 8. Which one of these fields (51,0,60) represent the base quality in this case? I am still confused about the ABI's SOLiD base quality!

                Any input is greatly appreciated!

                Comment


                • #9
                  Did you see the SAM FAQ?
                  http://sourceforge.net/apps/mediawik...pileup_output.

                  Hope this helps.

                  Comment


                  • #10
                    Hi Bruins,
                    Thanks for this very useful link. It definitely answers some of my questions.
                    -Uma

                    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
                    8 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, Yesterday, 06:07 PM
                    0 responses
                    8 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 03-22-2024, 10:03 AM
                    0 responses
                    49 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