samtools/sed for editing bam file

Question

[simo017]

I have the following sed command that change the chromosome name:

for file in /myoldpath/*.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 - $file > /mynewpath/${filename}_chr.bam
done

My quesion is how to insert the result in a new path while keeping the variable $filename as part of every new file name? it always insert the result in /myoldpath/ or literally "filename.chr.bam" in the /mynewpath/ am i missing something in the syntax of that part "$file > /mynewpath/${filename}_chr.bam"?

thank you in advance

[simo017]

Thank you @Goutham

[GenoMax]

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Answer 1

[GouthamAtla]

This should work.

for file in /myoldpath/*.bam
do
filename=`echo $file | awk -F"/" '{ print $NF}' | cut -d "." -f1 `
samtools view -H /myoldpath/$file | sed -e 's/SN:([0-9XY])/SN:chr\1/' -e 's/SN:MT/SN:chrM/' | samtools reheader - /myoldpath/$file > /mynewpath/${filename}_chr.bam
done

Its better to say:

filename=` echo $file | awk -F"/" '{ gsub(".bam" ,"", $NF); print $NF}' `

P.S There are many ways todo this, but I just want to modify your command, so that you understand it easily.