Pipe BBMap reformat output into SAMtools

Question

[bruce.moran]

Hi all,

I am wondering if I can pipe output from reformat.sh in BBMap into SAMtools view. My goal is to take a set of fastq and return an unaligned BAM headed with sequence dictionary (this is for use in GATK4). Using some GATK test data this part works (of course!):

bbduk.sh in1=6484_snippet_1.fastq in2=6484_snippet_2.fastq trimq=30 out=stdout.fq | reformat.sh in=stdin.fq out=stdout.bam

I suppose the question then is: can I force reformat.sh to produce a BAM without specifying ".bam" ending? Or, what form does 'stdout.bam' take and how can SAMtools recognise it? Or, can reformat.sh do the reheader itself?

All help much appreciated,

Bruce.

[Santosh Anand]

See Piping and Screen Output at https://github.com/BioInfoTools/BBMap/blob/master/docs/UsageGuide.txt#L18

[bruce.moran]

OK, I had read that, just tried a few things and it seems you have to stream through samtools view:

reformat.sh in=6484_snippet_1.fastq out=stdout.bam | samtools reheader 6484_snippet_header.sam - > 6484_snippet.rh.bam

returns [W::hts_close] EOF marker is absent. The input is probably truncated.

reformat.sh in=6484_snippet_1.fastq out=stdout.bam | samtools view -hb - | reheader 6484_snippet_header.sam - > 6484_snippet.rh.bam

returns a reheaded BAM! Thanks for the response and making me think a bit more.

Answer 1

[bruce.moran]

To answer my own Q:

bbduk.sh in1=6484_snippet_1.fastq \
          in2=6484_snippet_2.fastq \
          trimq=30 out=stdout.fq \
| reformat.sh in=stdin.fq \
               out=stdout.bam \
| samtools view -hb - | samtools reheader 6484_snippet_header.sam - > 6484_snippet.rh.bam

[Brian Bushnell]

Incidentally, you can skip the reformat step - bbduk.sh will allow "out=stdout.bam" also :)

[bruce.moran]

Cool, I had to use addslash and underscore hence the reformat.sh, but good to know.

[Brian Bushnell]

Ah, I see. Well, alternately, reformat.sh supports quality-trimming, so I guess it's bbduk that was unnecessary (unless you were doing a kmer-based operation).

[bruce.moran]

Thought about that also, but yes, using kmers.

[Brian Bushnell]

You have learned everything I have to teach,

[bruce.moran]

My RTFM is strong (also helps that there is a good FM)