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Can not find idels!!

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  • Can not find idels!!

    Hi guys
    I know that there will be a trivial answer to my question but I really can not understand where the problem is. I am aligning a 20x coverage Illumina paired end reads by using soap aligner. The command I am using is the following:

    ./soap -D ./reference.fasta.index  -a ./s_2_1_sequence.txt -b ./s_2_2_sequence.txt -o s_2_paired_mapped -u s_2_unpaired_reads -2 s_2_unpaired_mapped -v 3 -m 100 -x 400 -r 1 -g 10
    I then concatenate the paired_mapped and unpaired_mapped (the real name should be single_mapped) and convert it with the tool available at the soapdenovo website. I then use the sam file to gather information about indel by using samtools:

    1) samtools import (to get a bam file)
    2) samtools sort (to sort it)
    3) samtools pileup -f reference.fasta -i file_name.bam

    With the last command I can not get any indel. I am not an expert but I think that no indel at all is not possible. Have you got any idea on what is going on here?

    thanks a lot for the help

    UPDATE: by looking at the soap aligner first output I realised that indels are present. This make me thing that the problem is the perl script soap2sam. I will try to call snp and indel directly with soapsnp.
    Last edited by scami; 10-07-2010, 10:42 PM.

  • #2
    Try the "-c" option in the "samtools pileup" command to call the consensus sequence.


    • #3
      Just added -c before the -i flag in the above samtools pileup command. Unfortunately nothing changed!



      • #4
        use another aligner


        • #5
          I agree,

          BWA, Novoalign and BFAST all do a good job with finding indels from short read alignments and all of these programs support native SAM output.

          Originally posted by lh3 View Post
          use another aligner