A bash question

Question

[whb]

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. especially the " at the end and the - after 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

[GenoMax]

That extra " at the end is not needed.

- at the end of samtools view command is ok. That indicates that the input to samtools view is coming from the bwa and is being piped in.

[cpad0112]

your reference file is in the root folder. I am not sure if that is best practice.

Answer 1

[lethalfang]

I would even sort the bam file on the fly as well, e.g.,

bwa mem -R '@RG\tID:READ_GROUP\tPL:PLATFORM\tLB:LIB\tSM:SAMPLE_NAME' ‐C ‐t 2 hg38.fa sample_R1.cut.fastq.gz sample_R2.cut.fastq.gz \
| samtools view -Sbh - | samtools sort -m 2G --threads 4 -o aligned.sorted.bwa.bam

[WouterDeCoster]

You don't need the samtools view there - you can pipe it straight to samtools sort

[lethalfang]

Really? I didn't know that. Is there any flag I needed on the sort function? I thought you couldn't pipe plain text into samtools hence the -b flag in samtools view.

[GenoMax]

No flag is needed.

By default, samtools tries to select a format based on the -o filename extension; if output is to standard output or no format can be deduced, bam is selected.