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  • #31
    I was wondering if vyellappa's query was resolved? I'm getting the exact same error when I run another program that calls samtools.

    Traceback (most recent call last):
    File "../conifer/conifer_v0.2/conifer.py", line 597, in <module>
    args.func(args)
    File "../conifer/conifer_v0.2/conifer.py", line 526, in CF_bam2RPKM
    iter = f.fetch(p_chr,p_start,p_stop)
    File "csamtools.pyx", line 771, in csamtools.Samfile.fetch (pysam/csamtools.c:8233)
    File "csamtools.pyx", line 702, in csamtools.Samfile._parseRegion (pysam/csamtools.c:7458)
    ValueError: invalid reference `chr1`
    Thanks!

    Comment


    • #32
      I should have been clearer earlier.In sam fetch line:

      Code:
      samfile.fetch('chr1', 100, 120):
      Replace 'chr1' with '1' if that's how its encoded in your bam.

      Comment


      • #33
        Different read numbers between samtools view -c and pysam fetch()

        Any idea why pysam.Samfile and samtools don't see the same number of reads in a bam file?
        Code:
        samtools view -c file.bam
        => 355.610

        Code:
        python
        >>> import pysam
        >>> bam=pysam.Samfile("file.bam")
        >>> N=0
        >>> for read in bam.fetch(): N+=1
        ... 
        >>> N
        => 329.366

        Thanks in advance

        Comment


        • #34
          Originally posted by syfo View Post
          Any idea why pysam.Samfile and samtools don't see the same number of reads in a bam file?
          Code:
          samtools view -c file.bam
          => 355.610

          Code:
          python
          >>> import pysam
          >>> bam=pysam.Samfile("file.bam")
          >>> N=0
          >>> for read in bam.fetch(): N+=1
          ... 
          >>> N
          => 329.366

          Thanks in advance
          Problem solved - no need to fetch:
          Code:
          for read in bam: N+=1
          => 355.610

          Comment


          • #35
            Can Pysam call variants on .sam files?

            Can Pysam call variants on .sam files?

            Comment


            • #36
              No, more or less everything needs a sorted BAM file. I assume you're the same person who asked this in various forms on biostars too. Why not just convert to a BAM file, sort and index it? That's not exactly difficult.

              Comment


              • #37
                Please tell how to compare 300 VCF files using PySAM or smth else and to generate nonshared unique SNPs?

                Comment

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