gatk Hardfilter Error

Question

[bestone]

Hello, I run the code but I got the Error. Could you pls help me with this issue? How can I fix it?

 gatk VariantFiltration
  -R reference. fasta
  -V input.vcf
  --filter-expression "FILTER == 'PASS' && (QUAL < 30.0 || QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0)"
  --filter-name "FILTER_NAME"
  -O filtered.vcf

[bestone]

A USER ERROR has occurred: Argument output was missing: Argument 'output' is required.

---

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. zsh: command not found: -R zsh: command not found: -V zsh: command not found: --filter-expression zsh: command not found: -O

[Pierre Lindenbaum]

the formatting is missing in your question. how do you break lines ? did you add a antislash at the end of the lines ? didn't you forgot the last antislash before your option -O ?

[bestone]

Actually, I didn't forget, I added it, I tried, then I removed it, but I still got an error.

[Pierre Lindenbaum]

show us the very complete command line, including the antislash, including the error.

[bestone]

gatk VariantFiltration \
   -R reference.fasta \
   -V input.vcf.gz \
   -O output.vcf.gz \
   --filterExpression "AB < 0.2 || MQ0 > 50" \
   --filterName "my_filters"
/Users/uguremre/opt/anaconda3/bin/gatk:80: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if len(args) is 0 or (len(args) is 1 and (args[0] == "--help" or args[0] == "-h")):
/Users/uguremre/opt/anaconda3/bin/gatk:80: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if len(args) is 0 or (len(args) is 1 and (args[0] == "--help" or args[0] == "-h")):
/Users/uguremre/opt/anaconda3/bin/gatk:117: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if len(args) is 1 and args[0] == "--list":
/Users/uguremre/opt/anaconda3/bin/gatk:301: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if call(["gsutil", "-q", "stat", gcsjar]) is 0:
/Users/uguremre/opt/anaconda3/bin/gatk:305: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if call(["gsutil", "cp", jar, gcsjar]) is 0:
/Users/uguremre/opt/anaconda3/bin/gatk:458: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if not len(properties) is 0:
/Users/uguremre/opt/anaconda3/bin/gatk:462: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if not len(filesToAdd) is 0:
Using GATK jar /Users/uguremre/opt/anaconda3/share/gatk4-4.0.5.1-0/gatk-package-4.0.5.1-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Users/uguremre/opt/anaconda3/share/gatk4-4.0.5.1-0/gatk-package-4.0.5.1-local.jar VariantFiltration -R reference.fasta -V input.vcf.gz -O output.vcf.gz --filterExpression AB < 0.2 || MQ0 > 50 --filterName my_filters

USAGE: VariantFiltration [arguments]

Edited by GenoMax : Remainder of message was redacted since it was a print-out of in-line help for this tool.

[bestone]

---

A USER ERROR has occurred: filterExpression is not a recognized option

---

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

[GenoMax]

A USER ERROR has occurred: filterExpression is not a recognized option

This is the only important message here.

Are you copying and pasting this command from a document? in macOS?

[bestone]

so how can I fix it?

[GenoMax]

Are you copying and pasting this command from a document? in macOS? Looks like something in your command is not being recognized as a proper option (hyphens or quotes).

[bestone]

I am using macOS. I got the command from the link https://gatk.broadinstitute.org/hc/en-us/articles/360037434691-VariantFiltration

[GenoMax]

This may sound odd but can you turn-off "smart quotes and dashes" option in System Preferences and then type the hyphens and quotes in command by hand?

[bestone]

I tried it but unfortunately, still not working

[GenoMax]

Are you getting the same error or has that changed?

[bestone]

yes the same error

[GenoMax]

Have you re-typed every hyphen, quote and = (including one in middle of --filter-expression_?

[bestone]

Yes I re-typed the manual

[GenoMax]

Can you take out the --filter-expression option and see if the command works?

[bestone]

it worked when I remove it

[GenoMax]

That goes to show that there is something incorrect about the option in your command line. You will need to fix that.

[bestone]

The example given in the documentation is wrong, the parameters are --filter-expression and --filter-name as listed below, not --filterExpression. I parameter names might have changed between versions and the example hasn't been updated" Michael replied below. I changed them. It. worked thank you so much for your help.

[GenoMax]

I guess you changed the command in the original post since?

I moved @Michael's comment to an answer. You can accept it (green check mark) to provide closure to this thread.

Answer 1

[Michael]

The example given in the documentation is wrong, the parameters are --filter-expression and --filter-name as listed below, not --filterExpression. Parameter names might have changed between versions and the example hasn't been updated.

[bestone]

Thank you so much it worked:)