Understanding SAM/BAM file specifications

The sequencing Alignment Mapping (SAM) file was designed to store the mapping data of a sample against a reference genome in a way that allow for easy downstream analysis.
In this video, I hope to go through the basic SAM file specifications based on the original documentation from Samtools. SAM file mostly consists of two sections, a header section that records information on the reference genome and experiential details, and an alignment section that records the individual nucleotide sequence difference between the samples and the reference.
Link to SAM specifications
samtools.github.io/hts-specs/...
Link to Slides
docs.google.com/presentation/...
Link to sample SAM file
drive.google.com/file/d/1zmyH...
drive.google.com/file/d/1SCu-...
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[@fatimaruna9855]

Great presentation, really helpful.

[@sujayayyagari9039]

you made my life more easier with this video. Thanks

[@sus-dw7xl]

Well presented and explained. It helped a lot.
Thank you. Keep it up...

[@cheng-hsianglu5916]

Thank you for this amazing explaination!

[@catherinepuellomora8041]

amazing explanation¡ thanks for your work :)

[@ozlemkalkan5167]

Thank you, great presentation. It helped a lot.

[@tonkjon6296]

Gracias, estoy aprendiendo a usar Samtools y tu video me ayudó mucho. Buena tarde, chato.

[@lekshmirk3252]

Nice presentation 👏

[@musicspinner]

stellar overview.

[@joshuathomas8673]

Great video, thanks a lot!

[@zahraiqbal7337]

very informative! thanks!

[@yewenli]

Good video!

[@NatarajanGanesan]

Very helpful

[@seyma2308]

perfect!

[@belindamontecalvo3015]

Thank you ..

[@uguremre3287]

thank you for this amazing video, I have a question. How can I convert to BAM file to VCF format?

[@LiquidBrain]

Not sure it this will work, but i found a tools in galaxy call (bcftools mpileup) that could directly do the conversion you need, just not sure if it will fit the purpose of you converting between the two formats.
Technically, BAM store aligment while vcf store mutations, but i believe you can convert BAM to fasta using (Samtools fastx), and use the resulting fasta to run another SNP detection tools to generate the vcf.
Hope this helps
-Brandon

[@PrincipioDiLandauer]

im making a SAM file validator. Where can i find some SAM examples? Maybe ones with headers and some without?

[@javiflaja4063]

x2

[@zuraizbutt6592]

raw data set of Arabidopsis thaliana from GEO. Put it into GALAXY and de-contaminate it. After filtering you are supposed to align it on the any of the prescribed reference and show the results (At least header).
can you help me sir?

[@LiquidBrain]

I think i made a video on Galaxy earlier doing that :) Sorry for the loud music
ua-cam.com/video/4EOJTEGWOiU/v-deo.html

[@tinacole1450]

Have you done the alignment with pysam? I am having some trouble with my alignment. The code is: samfile = pysam.AlignmentFile(files, "rb") . It doesn't like the call of the files.. error msg : IsADirectoryError: [Errno 21] could not open alignment file `bam/`: Is a directory

[@LiquidBrain]

sorry havent tried pysam, but i will try to have a look once i got sometime