Convert UCSC BAM file to Ensembl

Question

[elad.zisman]

Hi, I'm looking for a way to convert my UCSC BAM files to an Ensembl format. Is there an easy way to do it? Thanks, Elad

[Pierre Lindenbaum]

how do you define an "Ensembl format" ?

[elad.zisman]

I have BAM files that where aligned to hg19 which is a UCSC assembly, and I what it to be aligned to grch37 instead, an ensembl assembly.

[Pierre Lindenbaum]

so you "just" want to change the chromosome notation ? Bam File: Change Chromosome Notation ; Change chromosome notation in bam file ; BAM File, Change chromosome notation ; Change Notation Of Chromosome In Bam File ; ....

[elad.zisman]

From what I understood the gene annotation is also different, but yes, the chromosome notation too.

[elad.zisman]

Thanks for the links. I now understand what I need to do!