A USER ERROR has occurred: Bad input: the IUPAC sample specified is not present in the provided VCF file

Question

[Vanuhi]

Hello all!

So I need a help. I am trying to make consensus files from vcf, with GATK FastaAlternateReferenceMaker. The python script I am using, takes my bam files as an input, calls variants for each individual by Freebayes, does minimum filtering after which takes generated vcf files to mask regions and make consensus files for each individual (with GATK FastaAlternateReferenceMaker; --use-iupac-sample ; as I need to include this info for my diploid samples).

I can't post the script, it's too long. But I get this error:

**********************************************************************

A USER ERROR has occurred: Bad input: the IUPAC sample specified is not present in the provided VCF file

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trac$
Using GATK jar /home/vanuhi/anaconda3/envs/190904_var_cons/share/gatk4-4.1.1.0-0/gatk-package-4.1.1.0-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 -Dsamj$
Traceback (most recent call last):
$odule>
    raw_cons_fa = SeqIO.read(raw_cons_fn, 'fasta')
  File "/home/vanuhi/anaconda3/envs/190904_var_cons/lib/python3.7/site-packages/Bio/SeqIO/__init__.py", line 730, in read
    raise ValueError("No records found in handle")
ValueError: No records found in handle

So as I get, generated vcf files doesn't include IUPAC encoding, which I need in my consensus files. Does anybody know how this can be fixed? Is there may be an option for Freebayes (which I couldn't find) to add the IUPAC ? Or should I add another step after calling vcf files, to encode them and then continue, and in this case how that can be done?

Thank you in advance, if needed more information I am happy to add.

[Pierre Lindenbaum]

--use-iupac-sample AS I

what is the output of

bcftools query --list-samples your.vcf | grep -w AS

if it is empty, then your command line is wrong as there is no such sample "AS" in the vcf.

[Vanuhi]

that AS is just a part from my text, I'll edit now.