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
1 answer
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
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Hi Pierre thanks to your answer.
I have another question what is the difference between sort and index?
http://www.htslib.org/doc/samtools.html
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...