Question: Which Parameters Are You Using For Samtools Mpileup And Bcftools To Compare Human Cells To See Individual Differences?
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Deniz • 180 wrote:
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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modified 6.8 years ago
by
Lars Juhl Jensen ♦ 11k
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6.8 years ago by
Deniz • 180
I edited your question to make sentences start with capital letters and not have almost every sentence end with multiple question marks.