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
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