Question: How to use "Mpileup" for getting information of the reads of the SNP from the BAM files?
gravatar for jigarnt
21 months ago by
jigarnt30 wrote:

Hi All,

I am thinking of using Mpileup from Samtools to get the information on the read quality and read depth from the BAM files. In that case which script should I use?

I have been recommended the script below:

ref=my_fasta.fasta samtools mpileup -f $ref -r chromosome_1:1018000-1018100 my_bam.bam my_bam2.bam

P.S. I dont have to do Variant calling, just need the read information.

Thanks in advance for your help.

mpileup snp bam genome • 726 views
ADD COMMENTlink modified 21 months ago by agata88660 • written 21 months ago by jigarnt30
gravatar for agata88
21 months ago by
agata88660 wrote:

I would not use mpileup at all - if you need only alignment statistics. Use BedTools. For example here : A: How to get coverage for an alignment file The read quality you can get from FASTQC

But to be clear:

First what you should do is to check your reads by FASTQC (if the quality is bad do trimming), then align them to reference and then perform BedTools.



ADD COMMENTlink written 21 months ago by agata88660
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