How to use "Mpileup" for getting information of the reads of the SNP from the BAM files?

Question

[jigarnt]

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.

Answer 1

[agata88]

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 http://www.bioinformatics.babraham.ac.uk/projects/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.

Best,

Agata