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
"at the end is not needed.
-at the end of
samtools viewcommand is ok. That indicates that the input to
samtools viewis coming from the
bwaand is being piped in.
your reference file is in the root folder. I am not sure if that is best practice.