Understanding SAM/BAM file specifications

[@sujayayyagari9039]

you made my life more easier with this video. Thanks

[@tonkjon6296]

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

[@sus-dw7xl]

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

[@fatimaruna9855]

Great presentation, really helpful.

[@ozlemkalkan5167]

Thank you, great presentation. It helped a lot.

[@cheng-hsianglu5916]

Thank you for this amazing explaination!

[@lekshmirk3252]

Nice presentation 👏

[@musicspinner]

stellar overview.

[@catherinepuellomora8041]

amazing explanation¡ thanks for your work :)

[@PrincipioDiLandauer]

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

[@javiflaja4063]

x2

[@NatarajanGanesan]

Very helpful

[@belindamontecalvo3015]

Thank you ..

[@zahraiqbal7337]

very informative! thanks!

[@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

[@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

[@seyma2308]

perfect!

[@yewenli]

Good video!

[@joshuathomas8673]

Great video, thanks a lot!