Examples/Exercises on SAMtools operating on BAM format

Question

[roccostorace]

Hello, i'm new in bioinformatics. Actually i'm studying what are the functions implemented by the SAMtools on the BAM format. To do this i'm studying functions from http://www.htslib.org/doc/samtools.html My goal is to understand and be able to use all the functions with the relative options (view, sort, ...)

So I have two questions to ask you:

1 - you have some material with many examples or exercises concerning these SAMtools functions to be used on the BAM

2 - someone kindly could make me a list of the most important functions: for example I imagine that view is very important, like the sort function. So to make me a sort of list with the main functions used

[roccostorace]

Hi Pierre thanks to your answer.

I have another question what is the difference between sort and index?

[Pierre Lindenbaum]

http://www.htslib.org/doc/samtools.html

samtools sort : Sort alignments by leftmost coordinates, or by read name

samtools index: Index a coordinate-sorted BAM or CRAM file for fast random access. This index is needed when region arguments are used to limit samtools view and similar commands to particular regions of interest.

[cschu181]

sort generates a bamfile that is either sorted by mapping coordinates (RNAME and POS, fields 3 and 4; default behaviour), by read name or by tags. index will then generate an index file, that contains information where in the bamfile you can find reads that map to a certain reference sequence. This is needed for random access, so that software like genome browsers can directly access specific regions without having to read through the whole bamfile. Index requires a bamfile to be sorted by coordinate.

edit: boo, too late...

Answer 1

[Pierre Lindenbaum]

you have some material with many examples or exercises concerning these SAMtools functions to be used on the BAM

toy* files under https://github.com/samtools/samtools/tree/develop/examples

convert to bam, sort, index, etc...

most important functions

samtools view samtools sort samtools index samtools faidx

imho