If I were you I'd just realign the data to the other genomes, but if for
some reason you really need to do this, use grglist() to get the alignments
as a GRangesList, then unlist it, and call rtracklayer::liftOver. It will
return a GRangesList, where each element corresponds to the input GRanges.
You'll need to account for the elements that are not length one (i.e., not
1-1 mappings). After that, you can form a GRangesList using the groupings
from the original grglist() result. Getting that back into a BAM will be
tricky though, but maybe the ranges are all you need?


On Sun, Sep 22, 2013 at 11:37 AM, rubi [guest] <guest@bioconductor.org>wrote:

>
> Hi,
>
> I have a bam file that was a aligned to a non-reference genome and I have
> the coordinate mapping between the non-reference and the reference genomes,
> either in a chains format or in the following block like format:
> #CHR    REF     NONREF
> chr1    1       1
> chr1    3003641 0
> chr1    3003645 3003641
> chr1    3003650 0
> chr1    3003654 3003646
> chr1    3006791 0
> chr1    3006793 3006783
> chr1    3006835 0
> chr1    3006836 3006825
> chr1    0       3007262
> chr1    3007273 0
> chr1    3007275 3007263
> chr1    0       3008478
> chr1    3008490 3008481
>
> Where the lines containing 0's indicate deletions (either in the ref or in
> the nonref).
>
> I would like to lift-over my bam from the non-reference to the reference
> which basically means lifting over the "pos" and "cigar" fields. Using the
> functions of GenomicRanges it is straight forward to do it for the "pos"
> field but it gets complicated for the "cigar" field. Any idea how can this
> be done efficiently?
>
>  -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] data.table_1.8.10    Rsamtools_1.10.2     Biostrings_2.26.3
>  GenomicRanges_1.10.7 IRanges_1.16.6       BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-5    parallel_2.15.2 stats4_2.15.2   tools_2.15.2
>  zlibbioc_1.4.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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