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FilterMutectCalls did not give any records with 'PASS' in the filter field
Hi, I used FilterMutectCalls to filter several VCF files one by one:
java -jar ~/gatk-126.96.36.199/gatk.jar FilterMutectCalls -V original.vcf.gz -O filtered.vcf.gz
And in every output file filtered.vcf.gz, there is no record with 'PASS' in the filter field.
I ran other tools on the same bam files, and they all output variants that passed their corresponding filters.
I use the default parameters when running FilterMutectCalls. It is strange that there are no variants in the filtered.vcf with 'PASS' in the filter field. Can you please help me how to fix it? Thank you!