Rename headers in BAM files

Moved from my old blog.

Now I am processing a batch of ChIP-Seq datasets, and got the datasets in bam format, and the headers of the chromosomes are “chr*.fa”, boring CASAVA suite. So for the fast way to remove “.fa” characters, I wrote the bash script:

for FILE in `ls *.bam`; do
    samtools view -H $FILE > header.txt
    sed 's/.fa//g' header.txt > new_header.txt
    samtools reheader new_header.txt $FILE > reheader/${FILE}
done

“convert_header.sh”