supplying multiple BAM files

[rajitz]

Hi,

I want to supply multiple BAM files to the cnv tool with the -I argument; I was able to do so with *bam, but I now want to limit it to only certain BAM files in the folder (without having to move them to a separate folder), and I tried to give it a text file with each BAM file listed line-by-line but that did not work. Please let me know the correct format for supplying multiple BAM files; i.e., how they have to be separated within the list of files given.

Thanks very much,
Rajat

[heuermh]

Hello @rajitz!

Spark uses Hadoop file system glob syntax for multiple files; see e.g.
https://hadoop.apache.org/docs/r2.4.1/api/org/apache/hadoop/fs/FileSystem.html#globStatus(org.apache.hadoop.fs.Path)

[rajitz]

That worked well, thank you!

Is it also possible to supply the BAMs in a separate file where they are all listed in a compatible format, instead of doing {file1.bam,file2.bam,file3.bam} ?

Thanks.

[heuermh]

If you're using a file with a list of BAMs, it looks like the format should be one BAM file per line

See
https://github.com/bigdatagenomics/deca/blob/master/deca-cli/src/main/scala/org/bdgenomics/deca/cli/Coverager.scala#L81

so your args should include -I list_of_bams.txt -l.

If you can't easily tell the difference between -{uppercase 'I'} and -{lowercase 'l'}, neither can I, whoever came up with those argument names ought to be shot. 😉

[rajitz]

Haha. That worked like a charm! Have a good weekend. Rajat

[rajitz]

Hi again, is there a way while doing this to just call CNVs on the first few samples listed instead of all of them? We don't want to have to spend time on calling CNVs in the reference set of samples. Thank you.