lucasl

Hi, I'm currently working with Genomestrip (version 3.7.GS-r1748-0-g74bfe0b) to do some structural variant calling on some BAMs that were aligned to hg38. Naturally, I used the resources available from the hg38 prerelease bundle for Genomestrip available here: ftp://ftp.broadinstitute.org/pub/svtoolkit/hg38_pre_release/ So far, whenever I use Genomestrip with hg38, I get several invalid interval errors. These appears to be legitimate intervals, so I'm not sure how Genomestrip is failing on these. Here are the intervals it fails on: chr22:24317068-24322453 chrY:10022097-10027150 chr21:20211411-20216694 I'd include a stack trace, but I've reached the max characters for one post. Any help would be greatly appreciated!

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lucasl
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  • OK, so I removed the line of code that was limiting the analysis to chr22, and also gave Genomestrip a list of all my BAMs, rather than a single BAM as I had done previously. What I found is that the subjobs started by Genomestrip in the PBS queue …
  • Hi, I tried using the official reference bundle, but I'm still getting the same error. I'm actually running Genomestrip on a BAM. My command line is: module load java/1.8.0_73module load jremodule load pbs-drmaacd /home/lochol/code/1kg-phase4./geno…