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  • #1

    How to call SNPs via samtools for sex-chromosome of diploid species

    Hi,

    I want to call SNPs for the sex chromosomes but autosomes via samtools for one diploid individuals.

    samtools mpileup -ugf ref.fa aln.bam | bcftools view -bvcg - > var.raw.bcf
    bcftools view var.raw.bcf | vcfutils.pl varFilter -D 100 > var.flt.vcf

    The SNP frequency of sex-chromosome is half of the autosomes, so I think maybe I need change some parameters?
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  • #2
    Help, please......

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