Split a SAM file

[rahul]

Hi All,

I am looking for a tool that can split SAM file into smaller sub SAM files. I just wanted to process(annotate reads) the SAM files in parallel and join them again? Do you think it is possible?

Thank you,

Rahul

[swbarnes2]

With samtools, you can generate sub bams by indicating what chromosome and positions you want in the sub file. Then you can convert back to sams.

[rahul]

Thanks for the immediate reply.I want to break the SAM file into smaller files based on the number of reads rather than chromosomal location. Still your method should do the work.

Thanks a lot.

Rahul

[severin]

linux split

The split function should do this for you though be sure that you are using a multiple of 4 or 8 depending on if it is paired end or not.

[rahul]

I have tried the split function and it does break the file. But SAM tools is unable to read the resulting subfiles. I am getting the following error when I try to sort the resulting subSAM file.


[bam_header_read] EOF marker is absent.
[bam_sort_core] truncated file. Continue anyway.
Segmentation fault

Please let me know if you have seen this errors before.

Thank you,

Rahul

[severin]

header

You have to be sure the header information is contained in the split files so you might have a separate header file that you can then add to each of the split files.

I have tried the split function and it does break the file. But SAM tools is unable to read the resulting subfiles. I am getting the following error when I try to sort the resulting subSAM file.


[bam_header_read] EOF marker is absent.
[bam_sort_core] truncated file. Continue anyway.
Segmentation fault

Please let me know if you have seen this errors before.

Thank you,

Rahul

[rahul]

Sure, That makes sense.Thanks a lot for all the help.

Rahul