Does BAM file from SRA contain aligned reads?

[cyber222]

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?

[gringer]

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?

That depends on your experience, available time, and domain knowledge.

I generally prefer doing my own read cleaning and alignment, because then I know precisely the process that was used for read filtering and mapping. From my own memory of how submissions work, I think the BAM files in SRA are aligned using whatever method the experimenter decided to use.

[mbblack]

As mentioned, the BAM files you download were prepared and uploaded by the submitter (FASTQ, while supported, is not a preferred format for SRA and is accepted as reference sequences for the aligned read files). So, if you read their methods and are happy with their QC cutoffs and mapping approach, you could use their BAM files. If not, you need to get the actual read files and do your own reference mapping.

Also take note of how old any submission is and what reference release they used. You may want to re-align the reads to a more recent reference build anyway.

A lot of times, yes, it would make little if any difference how you proceed. Sometimes though, it might. Look through the information provided about the submission and decide for yourself how you wish to proceed.