Question: Which Parameters Are You Using For Samtools Mpileup And Bcftools To Compare Human Cells To See Individual Differences?
gravatar for Deniz
6.8 years ago by
Deniz180 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/ 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!


bcftools mpileup • 2.9k views
ADD COMMENTlink modified 6.8 years ago by Lars Juhl Jensen11k • written 6.8 years ago by Deniz180

I edited your question to make sentences start with capital letters and not have almost every sentence end with multiple question marks.

ADD REPLYlink written 6.8 years ago by Lars Juhl Jensen11k
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