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  • samtools mpileup fails

    Hello all,

    I'm using asmtools mpileup for snp calling from eight bam files, I get this following error message

    bam2bcf_indel.c:181: bcf_call_gap_prep: Assertion `n_types < 64' failed.
    [bcf_sync] incorrect number of fields (7 != 5). Corrupted file?
    [afs] 0:16195.241 1:1.758 2:87.006 3:1.843 4:16.294 5:0.378 6:3.137 7:0.193 8:4.107 9:0.037 10:0.005 11:0.000 12:3.000
    13:0.000 14:2.008 15:0.118 16:10.874

    Any helps?

    Thanks

  • #2
    I thought this should never happen, but it happened... This says that at a position there are more than 64 types of indels. For now, you may use "-I" to disable indel calling.

    Comment


    • #3
      Originally posted by lh3 View Post
      I thought this should never happen, but it happened... This says that at a position there are more than 64 types of indels. For now, you may use "-I" to disable indel calling.
      Thank you heng,

      But I still get outputs, there are SNPs and INDELs in vcf file, can I trust them? Does samtools ignores the problem INDELs and complete the job, or stop running?

      Comment


      • #4
        No, your results are truncated.

        Comment


        • #5
          Originally posted by lh3 View Post
          No, your results are truncated.
          Yes, you are right. I get more variants with -I option on chr:MT.

          Comment


          • #6
            I am also getting this error. I wonder if it would be possible to somehow sort out positions with excessively many indels before running mpileup.

            Comment


            • #7
              Hi! lh3,

              I got similar error:
              [bcf_sync] incorrect number of fields (0 != 5). Corrupted file?
              [afs] 0:0.000

              What does this mean?

              Thanks

              Comment


              • #8
                Another error message when do the first step for SNP call using samtools:
                samtools mpileup -uf reference.fna sample.sort.bam |bcftools view -bvcg - > var.raw.bcf
                [mpileup] 1 samples in 1 input files
                samtools: bam_plcmd.c:596: group_smpl: Assertion `id >= 0 && id < m->n' failed.
                Aborted
                :-(

                Any suggestions?

                Comment


                • #9
                  You have read groups undefined in the header

                  Comment


                  • #10
                    Thanks! It works now!

                    BTW, I also tried the old "pileup" for SNP/INDEL call with my deep sequencing data (50000+). Somehow, the pileup out only count 8000 read depth (column eight of the pileup output) for the first reference base. And then add one more read for every next base(like 8001 for second reference base, 8002 for third reference base, and so on). Any suggestions(I already give the -d60000 option to increase the max read depth. It works for mpileup, but not for pileup)? Thanks.
                    Last edited by Haiqing; 03-21-2011, 03:40 PM.

                    Comment


                    • #11
                      How did you fix the read group issue? I am getting the same error: "bam_plcmd.c:596: group_smpl: Assertion `id >= 0 && id < m->n' failed" ...

                      Comment


                      • #12
                        I think I just removed these @RG header from SAM file(I do not use the read groups in my case).

                        Comment


                        • #13
                          Is there anyway to avoid using the -I option? I would still like to call the INDELs on my file. My error is:

                          [bcf_sync] incorrect number of fields (6 != 5) at 0:33736084
                          [afs] 0:27544.812 1:16105.314 2:36880.874

                          Comment


                          • #14
                            How can I implement the -I option? I've tried:

                            /u/local/apps/samtools/0.1.11/samtools mpileup -I -uf hg19.fa accepted_hits.bam

                            and

                            /u/local/apps/samtools/0.1.11/samtools mpileup -ufI hg19.fa accepted_hits.bam

                            and I still get the same error:

                            [bcf_sync] incorrect number of fields (8 != 5). Corrupted file?

                            Comment


                            • #15
                              Hi,

                              How did you solve this error, samtools: bam_plcmd.c:596: group_smpl: Assertion `id >= 0 && id < m->n' failed ? I am repeatedly getting this error! I have a merged and sorted bam file, which I am using to call SNPs using bcftools. i merged multiple sorted bam files using a "rg.txt" file I created..

                              Where should I look first ?

                              Thanks for any help!

                              aarti

                              Comment

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