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  • Novoalign inappropriately softclipping?

    I have downloaded some exome data that appears to have been aligned using Novoalign
    I determined this from the header:

    @PG ID:novoalign VN:V2.06.09 CL:novoalign -c 16 -o SAM -o SoftClip -r Random -f 1.fastq 2.fastq -d /home/vg37/genomes/hg18_nohaps.fa.novocraft

    When looking at the data in IGV, I see that lots of reads have a large fraction of the sequence softclipped, resulting in cigar strings such as "7S36M58S". The image below shows a region of the genome where this is particularly bad. I noticed that the softclipped sequences often match the genome sequence. I'm wondering why these regions were softclipped in the first place. Is this a known bug?

    Ryan


  • #2
    Softclipping

    Hi,

    I've been back through the change logs and can't find any record of fixing a bug that might cause this. Large amounts of soft clipping like this could be caused by low base qualities especially if quality is 2 (#) as we treat this almost like an N. In browser were you shading bases by quality?

    Colin

    Comment


    • #3
      BAM Extract

      Could you send be a extract (samtools view) from the bam file for the region you displayed and I'll take a look at it. Email to support at novocraft-dot-com.
      Colin

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