Hi,
I have scaffold level data, and I know the chromosomal assignment of each scaffold, and am trying to rename each scaffold to each chromosome it belongs to.
Here's the command I tried to rename one scaffold to chromosome 1 as a test:
samtools view -h s2907.bam |sed -e 's/SN:QRBIO1000092.1/SN:chr1/' | samtools reheader - s2907.bam > test_s2907.bam
It appears to work, but then when I check the test_s2907.bam file, the original scaffold name (QRBIO1000092.1) is still there, not the new chromosome name (chr1) I tried to assign.
I'd appreciate any help.
Thanks.
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written
by
truebeliever24 •
1 answer
Giving the -c option to samtools reheader seems to work:
samtools reheader -c 'sed -e "s/SN:QRBIO1000092.1/SN:chr1/"' s2907.bam > test_s2907.bam
While this worked for me it doesn't seem to be the most efficient way to do it. Rather the reheader docs say you can use a SAM file with a template header to replace the header in your BAM file in place, which seems like it would be much more efficient (if you need that).
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