[bharati]

Sorting bam file

How can I sort my bam file according to read headers. Kindly Reply soon.

[gringer]

using the '-n' option will sort by read name:

samtools sort -n <infile.bam> <out.prefix>

Run 'samtools sort' without any options to see more help.

[Charitra]

Is there a single command to sort .bam output of tophat "samtools sort aln.bam aln.sorted"

or there is a bunch of commands which I have to use... ?

any idea please ?

using the '-n' option will sort by read name:

samtools sort -n <infile.bam> <out.prefix>

Run 'samtools sort' without any options to see more help.

[gringer]

Is there a single command to sort .bam output of tophat "samtools sort aln.bam aln.sorted"

The tophat output should already be sorted... assuming you meant bowtie/bowtie2, all the samtools programs support piped input using '-' as a file name, so it's quite easy to sort your output without intermediate files using Linux pipes:

bowtie2 <options> | samtools view -S -b - | samtools sort - output.sorted

[yaseen.ladak]

Hi All

I have a question. I wish to run bowtie over 3 cores and get an output of aligned sorted and indexed bam files.

bowtie2 -p 3 -x ../genomes/hg38/hg38 -1 tg/1/S1R1_val_1.fq.gz -2 tg/1/S1R2_val_2.fq.gz | samtools view -Shu - | samtools sort - - | samtools index > bam/S1_srt.bam

The above command just foes till sorted how can I also include a index via the pipe such that I get a sorted aligned bam and also the index in the same pipe?

I look forward for your help.

Thanks,

Yaseen

[Richard Finney]

I don't think "samtools index" can handle piped input .

[blancha]

It makes no sense to pipe the output of samtools sort to samtools index.
You want to save the output of samtools sort.
Just save the output of samtools sort, and then index.
If you want a one line command, just put a semi-colon after the call to samtools sort, and them call samtools index.

This is also a duplicate post.

https://www.biostars.org/p/12747/

The same answer is posted just above your duplicated post on biostars.

[gringer]

I don't think "samtools index" can handle piped input .

Well, you can shoehorn around that by using anonymous files (and tee, where duplicated output is required):

samtools index <(samtools view -h ../out.aaa.bam | samtools view -Shu - | samtools sort -T . -O bam -o - | tee out.bam) out.bam.bai

Unfortunately, some programs still need to use seek for file processing, and that means code like this won't work. It seems like samtools index is failing for another reason here though:

Samtools-htslib-API: bam_index_build2() not yet implemented
Aborted

[daanum]

How can i sort multiple BAM files using samtools?

Hi,

Is there any way to sort multiple bam files at the same time using samtools?
Thanks.