hg19/hg19 liftover

[Oscar.K]

greetings all!

I am having some issues getting annotations for my sequences.
As it stands I have 14 BACs and fosmids as .bam and they overlap on a limited stretch of 300kb around the gene we are interested in, they came pre-aligned to an arbitrarily named reference .fasta which is an extracted sequence of the hg19 (all this was outsourced and was delivered to us).
What I want to do is to liftover all the data from these extracted ref sequences to the proper hg19 so that I can see annotations properly when viewing the data in IGV.
How is the best way to implement this, since the header of all the bams is linked to the name of the extracted ref sequence, but i know the exact chromosomal location (start-end) of the extracted sequence. So can this be done in a simple way?

grateful for any answers, tips or hints
best regards,
//Oscar

[Brian Bushnell]

If it's just 14 sequences, then you could do it by hand. Just use samtools to convert the bam to sam, then open it with a text editor. All you'd need to do is change the rname field to the name of the chromosome in the HG19 reference, and add an offset (the extracted sequence start) to the pos field. You would also need to replace the header with the header of an actual sam file generated from HG19.

Then convert back to bam with samtools.