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  • gaps in consensus built from samtools pileup

    Hi,
    I am a newbie to NGS data.

    I was trying to extract consensus from BAM files of 1000genomedata (namely ftp://ftp-trace.ncbi.nih.gov/1000gen...e.20100125.bam 8:125807080-126007080) by samtools pileup consensus calling (ref: hg19 human_g1k_v37.fasta.gz )

    I found some bases/positions like bases between position 125906527 and 125906541.

    What might be the reason?
    Can you guys please help me to obtains those missing bases?

    Thanks a lot,
    Culmen
    Attached Files
    Last edited by culmen; 07-21-2010, 09:14 AM.

  • #2
    The gaps means uncovered genomic positions. The sites without reads are not reported.

    Comment


    • #3
      thanks a lot for your reply.

      The gaps means uncovered genomic positions. The sites without reads are not reported.
      I do understand that sites without reads are not reported.

      But when I view that portion in ensemble genome browser of 1000 genomes, I can see consensus bases and coverage at those locations as shown here. ( either there must be some way to get that consensus bases or that browser might be using some other data )

      Comment

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