[dpryan]

my header.sam file looks OK. "chr" has been added.

But when I run the samtools reheader command, nothing changes in the original .bam file...

The reheader command doesn't change the original file (I'm not surprised you thought it would, the name lends itself to that belief and I don't think the documentation mentions this). You'll need to output things to a file rather than to samtools view. Try something like:

samtools reheader header.sam sample1.bam > sample1.fixed.bam

[mra]

BAM to BAM plus "chr"

The chromosome names can be changed on the fly. This command takes an input BAM file with chr names '1, 2, 3,..,X, Y, MT' and output a BAM file with names 'chr1, chr2, chr3,..., chrX, chrY, chrM' on both read and header lines. The output BAM doesn't include any non-canonical chromosome that could be present in the input BAM (such as JG*, Un*, etc).

samtools view -h INPUT.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0}  $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > OUTPUT.bam

[neurongs]

thank you mra for this useful tool!

[petervangalen]

The following line works well for me. It will replace the names of chromosome 1 to 22, X, Y and MT (mitochondrial DNA). It will create a new file with the name test_chr.bam instead of test.bam

use Samtools
samtools view -H test.bam | sed -e 's/SN:\([0-9XY]\)/SN:chr\1/' -e 's/SN:MT/SN:chrM/' | samtools reheader - test.bam > test_chr.bam

If you want to do this for a bunch of bam files at once, use a loop. The variable $filename is your file without the extension (assuming there is no period except the one in ".bam").

for file in *.bam; do filename=`echo $file | cut -d "." -f 1`; samtools view -H $file | sed -e 's/SN:\([0-9XY]\)/SN:chr\1/' -e 's/SN:MT/SN:chrM/' | samtools reheader - $file > ${filename}_chr.bam; done

[a_l_25]

stack in the output part

how to put the filename variable in different path than the original path where bam files located. Hence , keeping the variable $filename as part of the every new bam file's name.

[petervangalen]

You can just replace "> ${filename}_chr.bam" with "> /new/path/${filename}_ch.bam".