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sorting multiple .bam files in linux cluster

I am working Linux cluster and ı have 1000 bam files under bam/ directory and they have pretty similar name bam_runid_bf2ff0593235864c9d423d28f1746a42d62df29e_0_0 and just first 0 changing into folder like 1,2,3,

I am wondering how can ı sort them as a single and merge them after indexing. I tried:

for f in bam/*_0.bam
do
  samtools sort -@ 7 $f ${f/bam/sorted}
done

what u advised but it did not worked. sorry ı am very new in this field .I generate a snakefile. When I try dry run with snakemake -n this error is shown

SyntaxError in line 2 of /cluster/lrcfs/2397405/projects/nanopore_testing/data/remoratrial/Snakefile: invalid syntax

When I type in working node same command samtools options are pop up my screen :( could you explain to me more simple? Thanks

bam samtools snakemake
• 2,261 views • link
updated by Ram Ram • written by fatih • fatih

Your samtools sort syntax is incorrect. it should be as follows (assuming rest of your loop is working as expected).

   samtools sort -@ 7 -o ${f/bam/sorted} $f

If there is snakemake involved (code for which you have not shown above) then there may be more to this than just samtools syntax.

• 0 views • link
written by GenoMax GenoMax

Should it be ${f/.bam/.sorted.bam} instead?

• 0 views • link
written by Medhat Medhat

1 answer

Hi all,

I find out that samtools default package (1.15.1) has issue with library (libtinfow.so.6: no version information availabl(required by samtools)) so if you change the version like 1.14.1, this command (for f in <folder>/*_0.bam; do samtools sort -@ 7 -o ${f/bam/sorted} $f; done`) is working fine.

• 0 views • link
updated by Ram Ram • written by fatih • fatih

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