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Published 20 hours ago • verified publisher icon vpc-ccg

Issues running svict

Open shahmj opened this issue 5 years ago • 3 comments

Hi,

I'm trying to run this on a regular bwa mem bam file. I noticed 2 issues:

  1. svict expects "SO:coordinate" as the third column but in the bam that I'm providing it is the fourth. Could you make this more generic?
  2. svict then failed on the second to last decoy contigs, after going through most of the other supercontigs; right on or after NC_007605 and the last one is hs37d5. I didn't get any error messages. Is this a known issue?

Thanks, Minita

shahmj avatar Apr 09 '19 14:04 shahmj

Hi, we will fix (1) shortly. For (2) did you use the latest commit already?

Thanks.

yenyilin avatar Apr 09 '19 18:04 yenyilin

I did a conda install yesterday. I don't see the version in the usage though.

shahmj avatar Apr 10 '19 03:04 shahmj

I am still having this issue, was it fixed?

jeffpbruce avatar Mar 26 '20 01:03 jeffpbruce