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