Morgan Sparks
- Total activity 10
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 0
- Subscriptions 3
Activity overview
Latest activity by Morgan Sparks-
Morgan Sparks created a post,
GATK Handling of Paralogs
I work on an organism that is highly paralogous (salmon). It generally functions as a diploid with occasional tetraploidy and numerous paralogs. I am trying to understand how GATK--particularly the...
-
Morgan Sparks commented,
Sounds good, thanks for the help!
-
Morgan Sparks commented,
As in sample_name1 sample_name1.g.vcf.gz.csisample_name2 sample_name2.g.vcf.gz.csisample_name3 sample_name3.g.vcf.gz.csisample_name4 sample_name4.g.vcf.gz.csi Or just sample_name1.g.vcf.gz.csisamp...
-
Morgan Sparks commented,
Thanks, that makes sense. I thought about that when I was reading the documentation, but I was confused as to what exactly put there. My file map has 134 samples, so do I just direct --read-index t...
-
Morgan Sparks created a post,
GenomincsDBImport Failed to create reader from file: An index is required, but none found., for input source:
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: gatk-4.2.2.0 b) Exact command used: while read -a linedo/home/sparks35/gatk-4.2.2.0/gatk --java-options "-Xmx36g -Xms36g...
-
Morgan Sparks commented,
Genevieve Brandt (she/her) that does seem to have fixed it, should I expect to have to do this with all ___Spark related commands in gatk? Thanks!
-
Morgan Sparks created a post,
markduplicatesSpark .bam.parts output error (directory already exists)
AnsweredJust to preface, I downloaded gatk into my remote cluster home directory because using the version hosted in our bioinformatic applications directory (v. GATK/4.2.2.0) was failing at setting up the...