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FastaAlternateReferenceMaker generate a reference fasta rather than my sample haplotype fasta

Hi, I am using the following command, wanting to generate haplotype fasta for 97 samples:
java -Xmx25g -jar $gatk -T FastaAlternateReferenceMaker -R $ref_genome -o new_output.fasta --variant $vcf

Here are what I did to my .vcf file:
1) I keep all the meta-information
2) I only select a specific region in my .vcf file (around SNP sites within 3Mb in the reference genome)

I attached a .zip file containing the first 120 lines of my .vcf file, I do not know how do deal with this error.
Looking forward to professional guidance, thank you!


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Can you please post the text of the error? I can't access the file you posted.
  • ezio_ljjezio_ljj chinaMember

    I upload this file again and rename its to .txt type, hope this will work,thank you for your replay

  • ezio_ljjezio_ljj chinaMember

    @Geraldine_VdAuwera said:
    Can you please post the text of the error? I can't access the file you posted.

    this is part of my file content, because I have 97 samples, so I had to cut some cause there is not enough space to display:




    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ERR173170.variant18 ERR173171.variant18 ERR173172.variant18 ERR173173.variant18

    Y-WTSI 8945487 . A C 251.52 PASS AC=80;AF=0.909;AN=88;DP=398;FS=0.000;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant17-variant23-filterInvariant29-variant32-variant33-variant34 GT:AD:DP:GQ:PL ./. ./. ./. ./.
    Y-WTSI 8946748 . C T 83.81 PASS AC=79;AF=0.898;AN=88;DP=452;FS=0.000;set=filterInvariant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant17-variant23-filterInvariant29-variant32-variant33-variant34 GT:AD:DP:GQ:PGT:PID:PL ./. ./. ./. ./.
    Y-WTSI 8947450 . C T 164.81 PASS AC=82;AF=0.911;AN=90;DP=389;FS=0.000;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant17-variant23-filterInvariant29-variant32-variant33-variant34 GT:AD:DP:GQ:PL ./. ./. ./. ./.
    Y-WTSI 8947741 . C T 302.43 PASS AC=80;AF=0.909;AN=88;DP=403;FS=0.000;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant17-variant23-variant32-variant33-variant34 GT:AD:DP:GQ:PL ./. ./. ./. ./.
    Y-WTSI 8948555 . T C 153.64 PASS AC=80;AF=0.909;AN=88;DP=416;FS=0.000;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant17-variant23-filterInvariant29-variant32-variant33-variant34 GT:AD:DP:GQ:PL ./. ./. ./. ./.
    Y-WTSI 8948841 . A C 268.53 PASS AC=74;AF=0.925;AN=80;DP=357;FS=0.000;set=variant2-variant4-variant6-variant7-variant8-filterInvariant9-variant10-filterInvariant11-variant17-filterInvariant23-filterInvariant32-variant33-filterInvariant34 GT:AD:DP:GQ:PGT:PID:PL ./. ./. ./. ./.

    I just kept a few meta information, is this okay for you? And I also re-upload a file in .text file type, hope that one can work, thank you very much

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    I don't understand what is the error. What do you think is wrong here?
  • ezio_ljjezio_ljj chinaMember

    @Geraldine_VdAuwera said:
    I don't understand what is the error. What do you think is wrong here?

    I do not know what is wrong, either. Are their other tools which can do this job? Or if it is not, maybe I can just write a script for this.Tank you for you kind reply.

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