Hi Valeriu,
Thanks for your reply. It's good to know you can pipe the -c option that
way.
With a bit of trial and error, I'd gotten something similar to work for me
to convert CanFam3 UCSC to ENSEMBL
Best,
Marsha
On Tue, Jun 22, 2021 at 10:46 AM Valeriu Ohan <v...@sanger.ac.uk> wrote:
> Hi,
>
>
>
> That particular regular expression is tied to Chr prefixed contigs and
> even if you could OR in a rule for matching SN:M, you would want to apply
> different context dependent transformations. Your best bet is with a two
> chained reheader transformations:
>
>
>
> samtools reheader -c 'perl -pe "s/^(@SQ.*)(\tSN:)Chr/\$1\$2/"' in.bam |
> ./samtools reheader -c 'perl -pe "s/^(@SQ.*)(\tSN:M)\t/\$1\$2T\t/"' - >
> out.bam
>
>
>
> *From:* Marsha Wallace <md...@cornell.edu>
> *Sent:* 17 June 2021 15:39
> *To:* samtools-help@lists.sourceforge.net
> *Subject:* [Samtools-help] Samtools Reheader help request [EXT]
>
>
>
> Hi,
>
>
>
> I'd like to use samtools reheader to convert bam files from UCSC ('chr'
> prefix) to ENSEMBL (no 'chr' prefix) chromosome names.
>
>
>
> The current documentation at
> http://www.htslib.org/doc/samtools-reheader.html
>
> gets me most of the way there with the example:
>
> - Remove “Chr” prefix
>
> samtools reheader -c 'perl -pe "s/^(@SQ.*)(\tSN:)Chr/\$1\$2/"' in.bam
>
>
>
> To complete the chromosome notation conversion, I also need to rename the
> mitochondrial chromosome from UCSC to ENSEMBL notation (M to MT). It would
> be ideal to do this in the same command as removing the 'chr' prefix.
> However, I'm not familiar enough with perl expressions to integrate a
> change in the above example, and whether the above example would need a
> pipe to the second MT expression, a second -c 'perl -pe' flag, or some
> combination of both.
>
>
>
> Given the existing examples in the samtools documentation, my guess is
> this kind of chromosome notation conversion is the most common use for
> Samtools reheader, so it may also be beneficial to include the solution for
> this MT conversion in the documentation.
>
>
>
> Thank you in advance!
>
>
>
> Marsha
> -- The Wellcome Sanger Institute is operated by Genome Research Limited, a
> charity registered in England with number 1021457 and a company registered
> in England with number 2742969, whose registered office is 215 Euston Road,
> London, NW1 2BE.
>
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