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  • how to call snps with samtools from 454.bam

    Hi there,

    I really like samtools for variant calling on Illumina.bam. However, now I have a GS Junior 454 data set. I aligned the reads via bwa bwasw and got a .sam alignment. I converted to .bam via samtools and inspected the alignment in igv. There clearly is a heterozygous SNV at (my positive control):

    chr17 29556283:G>T

    This position is covered by 859 reads, 52% showing the reference base G and 47% the alternating T.
    I tried every modification/parameter tuning in samtools mpileup I can think of. BUT I CANNOT GET THIS VARIANT.
    If anyone would like to try please write me a line and I will send the .bam file (MID1.bam 515K, MID1.bam.bai 1.3M)

    I would really appreciate your help!

    peter

    p.s: sent email to [email protected] with subject e.g. snp calling on 454.bam

  • #2
    Try posting to the samtools help mailing list ([email protected]).

    Comment


    • #3
      Hi Peter,

      I just gave it a quick shot and looked it up on UCSC GB (assuming you are working with hg19/GRCh37 build). Seems that there are some segmental duplications. This could lead to alignment on multiple sites and possibly samtools discards these sites (I don't know for sure...).

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