Which parameters are you using for samtools mpileup and bcftools to compare individual SNP differences?
Could you write your commands?
I am using:
samtools mpileup -ugf *.fa *.bam *.bam *.bam *.bam
bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | bcftools/vcfutils.pl varFilter -D100 > var.flt.vcf
My question how can I improve my command to get best quality SNPs?
mpileup -ugf ?
What about -6 option or -6 -uDSf? I really appreciate any help!
thanks
Could you write your commands?
I am using:
samtools mpileup -ugf *.fa *.bam *.bam *.bam *.bam
bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | bcftools/vcfutils.pl varFilter -D100 > var.flt.vcf
My question how can I improve my command to get best quality SNPs?
mpileup -ugf ?
What about -6 option or -6 -uDSf? I really appreciate any help!
thanks
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