change name of scaffold to chromosome in .bam file

Question

[truebeliever24]

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.

[truebeliever24]

Any help is appreciated.

Answer 1

[seidel]

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).