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  • mpileup and multiple input files

    Hi All,

    Is there any reason why the order in which .bam files are given to mpileup would affect the number of sites in the mpileup file?

    I have 8 .bam files and I need to have an mpileup file with the samples in a particular order in the columns. I have run mpileup twice with the following settings:

    Code:
    samtools mpileup -d 1000000 -I -f in_genome.fasta 1st.bam 2nd.bam ... > out.mpileup
    When I run it again with a different order of the input .bam files I get a massively different mpileup file that then affects how many SNPs are called/analysed downstream.

    I am using samtools version 0.1.19

  • #2
    I've no idea, but you should use samtools-1.2 as 0.1.19 is pretty ancient now.

    Comment


    • #3
      Thanks jkbonfield. I'll try updating in case it's just a version issue. Still seems like odd behaviour though.

      Comment


      • #4
        I have now tried with the newer version of samtools (v. 1.2). This at least gives me mpileup files that are the same size. Hopefully this was just a weird version bug. We'll see what the downstream analyses turn up.

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