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Old 03-18-2017, 04:32 PM   #1
cyber222
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Location: Russia

Join Date: Mar 2017
Posts: 1
Default Does BAM file from SRA contain aligned reads?

Hello, everyone. I need to do SNP calling for the first time, so I have a couple questions.
For example, I want to use this sample https://trace.ncbi.nlm.nih.gov/Trace...run=SRR1295568

I can download from there reads in FASTQ format, align them on the reference genome using BWA, for example. After that I will get SAM file, then BAM file and so on.

But also, I can download BAM file from SRA(you choose this option on the bottom line).
As I understand, this file already contains aligned on the reference genome reads. So you don't need to align them, this work is already done, just launch SAMTools, bcftools and do SNPcalling.

So, my questions:
1) Am I right?
2) If Yes, is it better to align reads by yourself, using BWA, or just download BAM file? Would be there some differences in result?
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