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I have problem with Hard Filtering, anyone to help?
Hi guys, I was trying to run the below command and I got an invalid error from my argument. I could not find any mistake in my command and have also regenerated my input raw SNPs file but error remain the same. I could not also find any thread that have addressed this problem. What do you think I am doing wrong? logfile=filtered.error gatk 3.7.0 \ -T VariantFiltration \ -R fasta.fa \ -V raw_SNPs.vcf.gz \ --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" \ --filterName "default_SNP_filter" \ -o filtered_SNPs.vcf \ 2> >(tee "$logfile")
ERROR Invalid argument value '2.0' at position 9. ERROR Invalid argument value '||' at position 10. ERROR Invalid argument value 'FS' at position 11. ERROR Invalid argument value '>' at position 12. ERROR Invalid argument value '60.0' at position 13. ERROR Invalid argument value '||' at position 14. etc..