Does BAM File Use Hg18 or HG19 Coordinates?

How do you tell which coordinates are used in a .bam file?  Well, its pretty easy.  Just pull the .bam file header up using Samtools

samtools view -H filename.bam

view raw bam_header.sh hosted with ❤ by GitHub

Then check out the rows that begin with @SQ followed by SN:chr## and LN:########.  Compare the lengths of a few of the chromosomes to the below list of lengths.  Whichever list the lengths match will indicate which coordinates are being used in the .bam file.

	Chromosome hg18 Length hg19 Length
	chr1 247249719 249250621
	chr2 242951149 243199373
	chr3 199501827 198022430
	chr4 191273063 191154276
	chr5 180857866 180915260
	chr6 170899992 171115067
	chr7 158821424 159138663
	chr8 146274826 146364022
	chr9 140273252 141213431
	chr10 135374737 135534747
	chr11 134452384 135006516
	chr12 132349534 133851895
	chr13 114142980 115169878
	chr14 106368585 107349540
	chr15 100338915 102531392
	chr16 88827254 90354753
	chr17 78774742 81195210
	chr18 76117153 78077248
	chr19 63811651 59128983
	chr20 62435964 63025520
	chr21 46944323 48129895
	chr22 49691432 51304566
	chrX 154913754 155270560
	chrY 57772954 59373566
	chrM 16571 16569

view raw gistfile1.txt hosted with ❤ by GitHub

Hope this is helpful in determining which coordinates are used in your .bam files.