# Errors urgent in variant filtering and insertsize **URL:** \ **Category:** Uncategorized\ **Tags:** gtn-tutorial, variant-analysis, vcf, snpeff\ **Created:** [January 31, 2023, 12:45am UTC](https://help.galaxyproject.org/t/errors-urgent-in-variant-filtering-and-insertsize/9376 "2023-01-31T00:45:23Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Zachary\_Ramsay](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/zachary_ramsay/32/3964_2.png) [@Zachary\_Ramsay](https://help.galaxyproject.org/u/Zachary_Ramsay)\ **Post date:** [January 31, 2023, 12:45am UTC](https://help.galaxyproject.org/t/errors-urgent-in-variant-filtering-and-insertsize/9376/1 "2023-01-31T00:45:23Z")
First I need to select variants that are exonic and not in the 1000 genomes project. The 100G is coded in columns 11 to 16 as a “.” or “” used when its missing and whether its exonic or not in column 6. I uploaded a wANNOVAR csv and converted it to tsv. Im the usibf the regular filter option and no matter how many variations of the below I use it wont work. 6==‘exonic’ and c11==‘.’ and c12==‘.’ and c13==‘.’ and c14==‘.’ and c15==‘.’ and c16==‘.’ Im also supposed to do a simple non coding variant filter on a vcf file from snpeff eff but I not see a column or any data specifically indicating exons or 1000G. How can I do ths? Next i tried collectinsertsizemetrics and Im getting this error /usr/local/bin/picard: line 5: warning: setlocale: LC\_ALL: cannot change locale (en\_US.UTF-8): No such file or directory Picked up \_JAVA\_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/048/054/48054991/\_job\_tmp -Xmx7g -Xms256m 00:13:00.688 INFO NativeLibra NEED help URGENTLY ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 10, 2023, 7:26pm UTC](https://help.galaxyproject.org/t/errors-urgent-in-variant-filtering-and-insertsize/9376/2 "2023-03-10T19:26:19Z")
Welcome, @Zachary_Ramsay Maybe you found these already? 1. Since the data is in tabular format, you can use general text manipulation tools to perform filters. > **[Galaxy Training: Data Manipulation Olympics](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html)** > > Galaxy is a scientific workflow, data integration, and da... 1. And, variant analysis tutorials are here. > **[Galaxy Training: Variant Analysis](https://training.galaxyproject.org/training-material/topics/variant-analysis/)** > > Genetic differences (variants) between healthy and diseas... If you are having problems with a specific tool, please ask a new questions and include more details so the community here can help. Items like the server where you are working, the exact tool name/version, parameters, and example data lines provide context. All would be included in a shared history link or you can post that information directly. Guidance is here: > **[Galaxy Training: Troubleshooting errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html)** > > Collection of tutorials developed and maintained by the w... ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 10, 2023, 7:26pm UTC](https://help.galaxyproject.org/t/errors-urgent-in-variant-filtering-and-insertsize/9376/3 "2023-03-10T19:26:39Z")
Closed on March 10, 2023, 7:26pm UTC