Thank you Sheila, I corrected the dbSNP file to match the hg19 reference "chr".
I ran GATK3 in this region as you suggested. Indeed, the reads I am missing have the tag "Failed realignment".
Thanks for your help!!
One thing I notice is that you have set the Java heap size to 180gb but only requested 128gb of memory. I would try again requesting 200gb if possible. Another possibility that other users have reported is your reference files may have truncated during transfer.
I would say you can safely run BQSR with only the normal variant sites. In general, the GVCF mode of HaplotypeCaller should be sensitive and not miss any potential normal variation. Have a look at this thread as well.
I updated it
I am experiencing the same issues since last night for various workflows.
Hi @amaro -
Can you share the workspace with the failed job with [email protected] and I'll take a look at the logs?
Yes - make sure you use bgzip, not gzip. The indexes are made with tabix. Alternatively, you can specify the output from any of the steps as a .vcf.gz, and GATK will properly compress and index
You should be able to use SelectVariants with --max-nocall-number.
Geraldine has said she can do it. I made a note for her in another ticket. She may get back to you on here soon.