Errors urgent in variant filtering and insertsize

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1

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

2

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.
  1. And, variant analysis tutorials are here.

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: