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  • Help! about Samtools mpileup output

    Hi all,
    I try to use Samtools to call SNPs. This is my first time to use mpileup. My output ALT column contains a bunch of "X". I really don't know what they mean. After I use bcftools with -bvcg parameters, I found all the data containing 'X' in ALT column were removed and I only got hundreds of SNPs per sample(~1Gb bam file).

    Can you help me to explain those 'X' and call more SNPs? Do you guys think this 'X' phenomenon is due to the alignment mismatch to more than 1 contigs?

    I used small contigs(~2 million contigs) as my reference genomes and aligned my reads to these contigs by BWA.

    Thank you so much!
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