Saving results of samtools fillmd option

[pm2012]

Hi

This is a very naive question but I am stuck here.
How do I save a file of samtools fillmd results. The results are displayed on the screen but I am trying to save it to a file. I have tried output redirection to a file but it gives me a segmentation fault error and only gives truncated file.

Any help is appreciated.

Thanks

[GenoMax]

Have you tried "-o filename" to see if that saves a file instead of output redirection?

[pm2012]

The -o option is not available.

[chadn737]

Maybe try the -u option and then try output redirection. The -u gives an uncompressed bam for piping, so if you use this I would think that it would work.

[EmmaB]

fillmd

Did anyone work out how to get the fillmd command to output to a file rather than the screen?

[GenoMax]

Unless anyone has a better idea this seems to work.

$ samtools fillmd file.bam ref.fa | tee file.sam

[dpryan]

Wouldn't it be simpler to just

samtools fillmd file.bam ref.fa > file.sam

or do people want the output printed to screen too?

[GenoMax]

@Devon: Person who started this thread had noted that simple redirection led to seg fault and a truncated file (though that may have been the case only for a specific older version of samtools).

In theory simple redirection should work as you show above but I did not test it today (with v.0.1.19).

[dpryan]

Ah, apparently I skipped over that part. "tee" makes vastly more sense then.