Hello,
I need to add CB tags to my bam files. Below is what I'm doing. I see the tags when I pipe to stdout but the tag is not written to the new bam. What is it that I'm missing? Thanks!
# $LINE is the path to the original input bam, there is one bam for each $cell
samtools view -h -b -o ${cell}.bam ${LINE} | sed -e "/^@/! s/$/ CB:Z:${cell}/"
# or
samtools view -h -b ${LINE} | sed -e "/^@/! s/$/ CB:Z:${cell}/" > ${cell}.bam
# or
samtools view -h ${LINE} | sed -e "/^@/! s/$/ CB:Z:${cell}/" | samtools view -hb -o {cell}.bam -
1 answer
samtools addreplacerg is for read groups. This is not what OP asked.
Just for reference, I ended up using
java -jar jvarkit.jar samjdk -e 'String c=record.GetReadName(); record.setAttribute("CB",c.substring(0,21)),return record;' $cell.bam
However, ideally I would like to use something like:
java -jar jvarkit.jar samjdk -e 'String c="$cell"; record.setAttribute("CB",c),return record;' $cell.bam
But I can't seem to find the right way to pass a bash variable to java. When I execute the line above I get a CB tag that is CB:Z:$cell, the $cell variable does not get interpreted. Do you know how to make samjdk interpret my $cell variable?
Thanks!
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Pierre Lindenbaum had written this: Adding optional tags to a BAM file
https://github.com/ruqianl/appendCB may also be useful.