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?
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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