Hi, I have a set of human exome data sequenced with Agilent Sureselect XT HS2. I am following the Best practice document https://www.agilent.com/cs/library/software/public/AGeNTBestPractices.pdf
On p.3 the example for bwa, just want to check if this is correct before starting the long process for alignment.
" at the end and the
samtools view -b
bwa mem ‐C ‐t 2 /hg38.fa trimmed_dir/sample_R1.cut.fastq.gz trimmed_dir/sample_R2.cut.fastq.gz | samtools view ‐b ‐ > aligned_dir/sample.bam"
Any advice would be appreciated! Thanks