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Old 06-01-2011, 09:28 AM   #1
skblazer
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Default 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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Old 06-06-2011, 07:19 AM   #2
skblazer
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Help, please......
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