Filtering of Haplotypecaller VC should only be done for the single-sample route

[amizeranschi]

Description of the bug

Basically a similar error as one reported not too long ago on the GATK forums:
https://gatk.broadinstitute.org/hc/en-us/community/posts/4412714547611-FilterVariantTranches-Error-no-variants-with-INFO-score-key-CNN-2D-

The fix mentioned on that page was to make sure that the VCF file passed as input to CNNScoreVariants was a proper VCF file, and NOT a GVCF file.

I've checked the file passed as input to FilterVariantTranches in the working directory where the error occurred, and it appears to be a GVCF file.

The nextflow command that I'm running is:

nextflow run nf-core/sarek -r dev -latest \
--input sample-sheet.csv \
--outdir sarek-test-jointVC \
-profile docker \
--max_time '336.h' \
--max_cpus '64' \
--max_memory '256.GB' \
--fasta ${main_dir}/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.fa \
--fasta_fai ${main_dir}/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.fa.fai \
--dict ${main_dir}/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.dict \
--save_mapped \
--save_output_as_bam \
--vep_cache ${main_dir}/reproducible-sarek-error/Saccharomyces_cerevisiae \
--bwa ${main_dir}/reproducible-sarek-error/bwa-index \
--igenomes_ignore \
--genome null \
--joint_germline \
--tools haplotypecaller,vep \
--dbsnp ${main_dir}/reproducible-sarek-error/Saccharomyces_cerevisiae.vcf.gz \
--dbsnp_tbi ${main_dir}/reproducible-sarek-error/Saccharomyces_cerevisiae.vcf.gz.tbi \
--dbsnp_vqsr '--resource:ensemblvcf,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae.vcf.gz' \
--known_indels ${main_dir}/reproducible-sarek-error/Saccharomyces_cerevisiae_indels.vcf.gz \
--known_indels_tbi ${main_dir}/reproducible-sarek-error/Saccharomyces_cerevisiae_indels.vcf.gz.tbi \
--known_indels_vqsr '--resource:ensemblsnps,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae_indels.vcf.gz' \
--known_snps ${main_dir}/reproducible-sarek-error/Saccharomyces_cerevisiae_snps.vcf.gz \
--known_snps_tbi ${main_dir}/reproducible-sarek-error/Saccharomyces_cerevisiae_snps.vcf.gz.tbi \
--known_snps_vqsr '--resource:ensemblindels,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae_snps.vcf.gz' \
--vep_out_format tab \
--vep_include_fasta

Command used and terminal output

No response

Relevant files

nextflow-error.log.txt

System information

No response

[FriederikeHanssen]

🤦‍♀️ good catch. I think a work around until this is fixed should be to add --skip_haplotypecaller_filter

[amizeranschi]

What does --skip_haplotypecaller_filter do, exactly? I couldn't find any mention of it on https://nf-co.re/sarek/dev/parameters

[FriederikeHanssen]

ah sorry, my mistake, actually it is --skip_tools haplotypecaller_filter ( i was looking in the wrong place myself)

[amizeranschi]

OK, I'll try running once with --skip_tools haplotypecaller_filter for testing purposes. But please, have a look if you can fix the GVCF issue as well, because we will actually require variant filtration for this joint calling use case.

[amizeranschi]

For the record, the pipeline finished successfully with --skip_tools haplotypecaller_filter.

[FriederikeHanssen]

Hey! Let's keep it open until the param thing is fixed or we will forget it :)

[amizeranschi]

Fixed in #1050.