[ensembl-dev] snp effect predictor for samtools consensus pileup; also, timeouts

[Michael Yourshaw]

The snp effect predictor perl script has problems with consensus format pileup files as generated by samtools with the -c option (http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#I_do_not_understand_the_columns_in_the_pileup_output). Specifically, it doesn’t seem to like indels (* in col 3) or heterozygous snps denominated by iupac ambiguity codes.

Attached is a revised script that takes care of theses issues. I have only been able to test it on a few files, so take with a grain of salt. In particular, I have not tested with any other file formats.

Another issue I have is that the sql connection times out with a buffer size of 500. A buffer of 100 seems to work, at least for a while. Is there a way to recover from a timeout? Or is there a mirror database closer to Los Angeles USA that might perform better than the default?



ॐ

Michael Yourshaw
UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu
970.691.8299

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