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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.

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @rrbutleriii

    I will ask the developers about this. In the mean time you could use the -se option(Regular expression to select multiple samples) to select for samples, so that your work is not interrupted.

    Regards
    Bhanu

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