Hello,
I am using samtools to generate a pileup file from a Mosaik genome assembly. My problem is that the pileup file contains all "N's" in the reference sequence field (column 3). I have double checked that I am using the exact same multi-sequence fasta file as the reference for both Mosaik and samtools.
Has anyone ever run into this before? I am using MosaikSort and MosaikText to generate a sorted bam file for input into samtools. Without the reference, I cannot get SNP quality scores, which is the whole point of my analysis.
Thanks for your help,
Sarah
[email protected]
I am using samtools to generate a pileup file from a Mosaik genome assembly. My problem is that the pileup file contains all "N's" in the reference sequence field (column 3). I have double checked that I am using the exact same multi-sequence fasta file as the reference for both Mosaik and samtools.
Has anyone ever run into this before? I am using MosaikSort and MosaikText to generate a sorted bam file for input into samtools. Without the reference, I cannot get SNP quality scores, which is the whole point of my analysis.
Thanks for your help,
Sarah
[email protected]
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