Homo Sapianes GRCh37 genomic coordinates

[papori]

Hi all,
I am looking for coordinate file of the GRCh37 genome.
My porpuse is to know what is the last coordinate in each chromosome.

For example if i am using "samtools view" function.

samtools view aln.sorted.bam chr2:20,100,000-20,200,000

How can i know if "20,200,000" is not out of the boundries?

Moreover, Do i have to sort the bam file before "view" specific coordinates?
Can i know from the bam file if its already sorted?

Thanks,
Pap

[papori]

i found this:

http://en.wikipedia.org/wiki/Human_genome

But i want for specific version.

[papori]

find it here:

http://jul2012.archive.ensembl.org/Homo_sapiens/Info/Index?db=core;r=7

[swbarnes2]

If you want a quick way to do it from the .bam itself, samtools idxstats will make a file that breaks down how many reads hit every chromosome, and it includes how long each chromosome is.

[papori]

If you want a quick way to do it from the .bam itself, samtools idxstats will make a file that breaks down how many reads hit every chromosome, and it includes how long each chromosome is.

Thanks!
Do you know how could i figure out if the bam sorted by read names or by chromosomal coordinates or not sorted?

[Brian Bushnell]

There should be a line in the header that looks like this:

@HD VN:1.4 SO:unsorted

That would be unsorted. It could also say "SO:coordinate" which would mean it was sorted by coordinates.

[papori]

There should be a line in the header that looks like this:

@HD VN:1.4 SO:unsorted

That would be unsorted. It could also say "SO:coordinate" which would mean it was sorted by coordinates.

Great! thanks

[papori]

Hi,
Can i get the sequencing coverage from the bam file?
Or, any other easy alternative?
Thanks

[Brian Bushnell]

Depends on what you want. If you want average coverage, just calculate (# mapped reads) * (read length) / (genome size).

If you want per-base coverage, you can get that from samtools pileup, I believe. The file has to be sorted. There are also other kinds of coverage, so what are you looking for, specifically?

[papori]

Depends on what you want. If you want average coverage, just calculate (# mapped reads) * (read length) / (genome size).

If you want per-base coverage, you can get that from samtools pileup, I believe. The file has to be sorted. There are also other kinds of coverage, so what are you looking for, specifically?

i think the first works for me!
Thanks