I am using RNA-seq data for SNP calling. I have used the Unified genotyper tool from GATK with this command:
java -Xmx22g -jar /bubo/sw/apps/bioinfo/GATK/2.3.6/GenomeAnalysisTK.jar -T UnifiedGenotyper -R path/to/myreference.fa -I path/to/mybamfile.bam -stand_call_conf 30 -stand_emit_conf 30 -o snps.raw.vcf
I have obtained SNPs mostly with very high phred scale but the filter field is "." for all my SNPs, there is no PASS or LowQual in the field. I read in the GATK forum that: " If the FILTER field is a ".", then no filtering has been applied to the records, meaning that all of the records will be used for analysis but without explicitly saying that any PASS. You should avoid such a situation by always filtering raw variant calls before analysis. "
I was wondering about the filtering process, is it a parameter that I should add to my command or I must do it in another way?
Thanks a lot for your help.