Which Parameters Are You Using For Samtools Mpileup And Bcftools To Compare Human Cells To See Individual Differences?
Which parameters are you using for samtools mpileup and bcftools to compare human cells to see individual 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? I really appreciate any help!
thanks
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Lars Juhl Jensen
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Deniz •
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I edited your question to make sentences start with capital letters and not have almost every sentence end with multiple question marks.