So I have used the latest GATK best practices pipeline for variant detection on non-human organisms, but now I am trying to do it for human data. I downloaded the Broad bundle and I was able to run all of the steps up to and including ApplyRecalibration. However, now I am not exactly sure what to do. The VCF file that is generated contains these FILTER values:
I am not sure what these mean. Does the "VQSRTrancheSNP99.90to100.00" filter mean that that SNP falls below the specified truth sensitivity level? Does "PASS" mean that it is above that level? Or is it vice versa? And what does "." mean? Which ones should I keep as "good" SNPs?
I'm also having some difficulty fully understanding how the VQSLOD is used.... and what does the "culprit" mean when the filter is "PASS"?
A final question.... I've been using this command to actually create a file with only SNPs that PASSed the filter:
java -Xmx2g -jar /share/apps/GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -T SelectVariants -R ~/broad_bundle/ucsc.hg19.fasta --variant Pt1.40300.output.recal_and_filtered.snps.chr1.vcf -o Pt1.40300.output.recal_and_filtered.passed.snps.chr1.vcf -select 'vc.isNotFiltered()'
Is this the correct way to get PASSed SNPs? Is there a better way? Any help you can give me would be highly appreciated. Thanks!