advice for running quip on exome BAM

dcjones / quip

Compressing next-generation sequencing data with extreme prejudice.

http://www.cs.washington.edu/homes/dcjones/quip/

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advice for running quip on exome BAM #6

Closed akiezun closed 12 years ago

akiezun commented 12 years ago

I'd like to try running quip on an exome file. I run this:

quip-1.1.0/src/quip -i bam -o bam -a -c $bam > $bamOut

and the result is a file only 1% smaller (and it's not a valid BAM file, nor can it be examined with quip --test or --list) so I guess I'm missing something. How should I run quip properly?

dcjones commented 12 years ago

It turns out there was a bug in how quip handled the headers of some BAM files. This is now fixed in version 1.1.1, which you can download here.

Specifying -i bam -o bam will convert a BAM file to a BAM file, so you should get the same thing out you put in. If not, please let me know.