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Combine a directory of GVCF files with gatk CombineGVCFs

I've produced a set of about 400 of GVCF files with gatk HaplotypeCaller, with the -ERC GVCF option. I'd now like to combine them for downstream genotyping and variant recalibration. I believe I can combine with gatk CombineGVCFs.

gatk CombineGVCFs \
   -R reference.fasta \
   --variant sample1.g.vcf.gz \
   --variant sample2.g.vcf.gz \
   -O cohort.g.vcf.gz

But what I don't know, is how to input all my 400 GVCF files into CombineGVCFs. I've heard this can be done with the --arguments_file option, but I don't know how to build such a file?

Any help gratefully received!

gatk combinegvcfs gvcf
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updated by DareDevil DareDevil • written by michael.flower.14 • michael.flower.14

2 answers

create a file with the .list suffix containing the path to your vcf

find /path/to/dir -type f -name "*.vcf.gz" > input.list

and then use this file with the '-V' argument

(...)    --variant input.list
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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you, that seems to allow CombineGVCFs to run.

gatk CombineGVCFs \
   --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' \
   -R "$GKREF"/Homo_sapiens_assembly38.fasta \
   --variant "$OUT"/temp_gvcf_2/input.list \
   -O "$OUT"/temp_gvcf_2/cohort.g.vcf

However, the resulting vcf file seems to only have one sample in it. The columns in the output are as follows:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  M00819_262_000000000-BP6CG_1_
chr1    12046   .   G   <NON_REF>   .   .   END=12410   GT:DP:GQ:MIN_DP:PL  ./.:0:0:0:0,0,0

I'd expected a column of genotypes for each sample (i.e. 400 columns)??

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written by michael.flower.14 • michael.flower.14

this is unrelated to the original question. Please, validate the answer.

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written by Pierre Lindenbaum Pierre Lindenbaum

You can try:

gatk CombineGVCFs \
  -R "$REFERENCE" \
  $(for f in $GVCF_DIR/*.g.vcf.gz; do echo -n "-V $f "; done) \
  -O "$COMBINED_GVCF"
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written by DareDevil DareDevil

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