We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

FastaAlternateReferenceMaker and useIUPAC

Hey,

I`m trying to use the option --useIUPAC with the FastaAlternateReferenceMaker. I tried several ways to set this option but all lead to ERRORs (see below). Without the option no ERROR message occurrs.

Here my code and...

java -Xms1g -jar "/home/GenomeAnalysisTK.jar" \
-T "FastaAlternateReferenceMaker" \
-R "/home/refGen.fa" \
-L "chromosome3" \
-lw "100" \
--variant "/home/chromosome3_raw_snp_filter3.vcf.gz" \
-o "/home/chromosome3.fasta" \
--useIUPAC 

the ways I used useIUPAC:

--useIUPAC
##### ERROR MESSAGE: Argument with name 'useIUPAC' isn't defined.

--useIUPAC "true"
##### ERROR MESSAGE: Argument with name 'useIUPAC' isn't defined.

-useIUPAC "true"
##### ERROR MESSAGE: Argument with name 'useIUPAC' isn't defined.

-useIUPAC
##### ERROR MESSAGE: Argument with name 'useIUPAC' isn't defined.

Best Answer

Answers

  • jenmodjenmod durhamMember

    What happens to ambiguous bases (hets) when the --useIUPAC flag is not added?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @jenmod In that case one allele will be chosen randomly.

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭

    Nope, that's not right. If the --useIUPAC flag is not added then it will always use the alternate allele (even if the sample is homozygous reference).

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Oh my bad, I was thinking of the case when there are multiple alternate alleles (eg ref is A and observed alts are C,T).

  • tstubertstuber Member

    Using version 3.4-0-g7e26428 I'm unable to get -IUPAC to work. The 3 arguments tried have been:
    --use_IUPAC_sample
    --use_IUPAC
    -IUPAC

    Executed command:
    java -jar ${GATKPath} -T FastaAlternateReferenceMaker -R ref.fasta -o output.fasta -V input.vcf --useIUPAC_sample

    The VCF used was created with HaplotypeCaller using default (2) ploidy.

    I would like to output a reference with ambiguity calls when AC=1 is between a specified QUAL range. The VCFs can be altered with IUPAC calls before loading into FastaAlternateReferenceMaker, but the call is then seen as malformed and unparsable. I would like to test -useIUPAC to see its interpretation of mixed calls. Am I using this tool incorrectly?

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @tstuber
    Hi,

    The issue is that you have to specify the sample name with -IUPAC. So, if you have the sample name as "sample1", you would specify -IUPAC sample1.

    -Sheila

  • tstubertstuber Member

    Wish I would have figured this out on my own. At least an easy fix. Thanks for the help!

  • biojenny08biojenny08 ColombiaMember

    Hi

    I am using exactly the same comand:

    java -jar ${GATKPath} -T FastaAlternateReferenceMaker -R ref.fasta -o output.fasta -V input.vcf --useIUPAC_sample

    However, I don´t understand what you mean with "sample" at the end of -useIUPAC_sample comand. The sample is again my vcf?

    Thanks

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @biojenny08
    Hi,

    You need to specify the name of the sample (RGSM). For example, if your sample name is NA12878, you would specify -IUPAC NA12878.

    -Sheila

  • nute11anute11a Member
    edited April 2018

    Hello, I'm having a similar problem. I'm using GATK version 3.6

    This was my error message:

    Argument '--use_IUPAC_sample' requires a value but none was provided

    this was my command:

    java -jar path/to/GenomeAnalysisTK.jar \
    -T FastaAlternateReferenceMaker \
    -R reference.fasta \
    -o output.fasta \
    -V variant_sampleID.vcf \
    --use_IUPAC_sample

    I also tried using the --useIUPAC flag you mentioned above and I got this error:

    Argument with name 'useIUPAC' isn't defined.

    ****UPDATE: I saw a comment posted above and added
    --use_IUPAC_sample sample_id
    and it seems to be running.

Sign In or Register to comment.