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Missing sample_file -sf option in GATK4 SelectVariants
In the port over to
gatk SelectVariants the sample name
-sn and sample expression
-se options made it in, but the sample_file
-sf option did not seem to make it. I tried:
gatk SelectVariants \ -V in.vcf.gz \ -O out.vcf.gz \ -RF SampleReadFilter \ -sample sample_list_file.txt
as a workaround, and it didn't have any errors, but the output file is more than three times the size of the input file, and still shows all the samples.