[ensembl-dev] variant effect predictor duplicate output lines

Michael Yourshaw myourshaw at ucla.edu
Sun Aug 28 21:53:59 BST 2011


I’m observing duplicate output lines with VEP under some cases. My test case is a VCF file with 32 variants involving 13 chromosomes. My command line is:

--buffer_size 5000 -input_file /Volumes/storage/vw/snp1_test.vcf --format vcf -output_file /Volumes/storage/vw/snp1_test.vcf.vep --force_overwrite --terms SO --sift=b --polyphen=b --condel=b --regulatory --hgnc --hgvs --protein --gene --check_ref --host localhost —no_progress

It looks like in whole_genome_fetch, at line 1437 &print_consequences($config, \@finished_vfs)is not clearing out @finished_vfs after calling print_consequences so the first time through it prints chr X, the second time chr X and chr 1, then X, 1, 2, etc.

adding an undef @finished_vfs; after this line seems to fix the issue.

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

This message is intended only for the use of the addressee and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are hereby notified that any dissemination of this communication is strictly prohibited. If you have received this communication in error, please erase all copies of the message and its attachments and notify us immediately. Thank you.





-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20110828/7c5be0b0/attachment.html>


More information about the Dev mailing list