I would like to visualise some of my bam files on IGV, the reference genome used to analyse was GRCh37. I do not find it on IGV is hg38 similar to GRCh37 or hg19 is the same.
Thanks in advance
hg38 is GRCh38. GRCh37 is hg19 (except for a base difference in the mitochondrial genome, if memory serves).
More information to add (courtesy MatthewP): GRCh37 / hg19 / b37 / humanG1Kv37 - Human Reference Discrepancies
In essence: GRCh37 is identical to hg19 on the main contigs (chr1-24), but differ on chrM, as per Devon.
Kevin
GRCh37d5 is different since there is a decoy sequence that may not be present in some hg19 builds. Also if memory serves me GRCh37 with or without decoy hard masks the pseudoautosomal regions on chrY, therefore you treat the pseudoautosomal region on chrX as diploid in males. I do not think some of the hg19 releases (UCSC I think) hardmask the PAR on chrY.
Hardmask just means there are "N" nucleotides in that region.
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Thank you so much. One more quick question Im new to bioinformatics and I would like to access .bam files on my computer to analyze using Terminal how do I copy dir and use data from my computer?
How you get the data to your own computer will depend on where it is. I suggest you talk to either your sequencing facility (if they're providing you with BAM files) or your system/cluster administrator if you were processing things on a remote server. Generally you would use sftp (or filezilla, if you prefer), but there may be more convenient methods (e.g., using NFS or SMB to not need to actually copy the files).
Thank you Devon Ryan