My command:
./gatk VariantFiltration -V ~/sample.vcf.gz -O ~/filtered.vcf.gz -R ~/reference2/Homo_sapiens_assembly38.fasta --filter-expression "DP >= 10 && MBQ >= 20"
it gives me a lot of variants out of my criteria in my condition. why and how to fix it ? the output I work on is the output of mutect
My command:
./gatk VariantFiltration -V ~/sample.vcf.gz -O ~/filtered.vcf.gz -R ~/reference2/Homo_sapiens_assembly38.fasta --filter-expression "DP >= 10 && MBQ >= 20"
it gives me a lot of variants out of my criteria in my condition. why and how to fix it ? the output I work on is the output of mutect