Hi All,

I am using bwa mem and samtools to get files in bam format. The cammand I am using is as follows:

bwa mem data/genome.fa data/samples/A.fastq ¦ samtools view -Sb - > aln.bam

I get an error:

mem: invalid option -- ´b´

However, these two commands work fine when executed separately.

Any leads as to what could be happening.

Thank you.