Stampy and BWA premapper

[rdeborja]

I recently downloaded v1.0.9 of Stampy and am currently running into an issue when attempting to use BWA as a premapper. I'm including the command that I've issued as well as the error that is displayed:

Command issued:
stampy.py --bwaoptions="-q10 hg18.fa" -g /UCSC_hg18/stampy/hg18 -h /UCSC_hg18/stampy/hg18 --sanger -M ../../syntheticData_qs/synthetic_76_NONE_20_1_0_chr22_152mer_100K.random.mod.fq > synthetic_76_NONE_20_1_0_chr22_152mer_100K.random.mod.fq.sam

Error:
stampy: Error: too many values to unpack

If I run stampy without the BWA premapper, there are no issues and alignment begins to populate the output file almost immediately. Any suggestions?

[zee]

The most recent mail I received from the stampy mailing list was that the authors removed the BWA option in the latest version.

[rdeborja]

Thanks for the note. Gerton got back to me and fixed the issue in a new release (i.e 1.0.10). The BWA option has been resolved. There is definitely a speed improvement when using hybrid mode.