Using gatk VariantFiltration to filter ONT wf-artic generated VCF files
Will it be valid to use gatk VariantFiltration on the variant calls generated using wf-artic pipeline? I am asking this because we have both Illumina and ONT runs for few samples and we wish to check overlaps of variants and I was thinking to process variant call files uniformly using the nextflow code chunk below. Since I haven't seen any pipeline handling long read data using any utility of GATK, I began to wonder if I should use it at all.
here is the nextflow code chunk
gatk SelectVariants -V ${vcf.toRealPath()} --select-type-to-include SNP -O ${sid}_snps.vcf
gatk SelectVariants -V ${vcf.toRealPath()} --select-type-to-include INDEL -O ${sid}_indels.vcf
gatk VariantFiltration -R ${params.ref} -V ${sid}_snps.vcf --filter-expression \"QD<2.0 || FS > 60.0 || SOR > 3.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" -filter-name \"bad_SNP\" -O ${sid}_filtered.snps.vcf
gatk VariantFiltration -R ${params.ref} -V ${sid}_indels.vcf --filter-expression \"QD<2.0 || FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" -filter-name \"bad_INDEL\" -O ${sid}_filtered.indels.vcf
gatk SelectVariants --exclude-filtered true -V ${sid}_filtered.indels.vcf -O ${sid}_good_indels.vcf
gatk SelectVariants --exclude-filtered true -V ${sid}_filtered.snps.vcf -O ${sid}_good_snps.vcf
gatk MergeVcfs -I ${sid}_good_snps.vcf -I ${sid}_good_indels.vcf -O ${sid}.mergeSNPsIndels.vcf
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Thank you for your post, rohit satyam ! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions.
Please see our Support Policy for more details about how we prioritize responding to questions.
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Hi. I was wondering if the GATK team was able to find time to review this query. I read your support policy and my question seems to be in the lowest priority category. But we are planning to submit the SARS-Cov-2 assembly to GISAID. So, in case if you can make an exception, please.
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Hi Anthony DiCi. It's been a month now. Is there any update from your team? Genevieve Brandt (she/her) Can you help me, please? I have long waited to get a "yes" or "np" reply to my query above.
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Hi rohit satyam,
Thank you for your much-appreciated patience! We have not yet gotten to your ticket as the number of questions like yours is significant. In the interest of fairness, we answer inquiries in the order in which they are posted. However, since you appear to have a deadline looming, I will make an exception for you this time.
I brought your inquiry to our developers and received some feedback to share with you. If you are asking whether VariantFiltration will filter VCFs generated from nanopore sequencing, the answer is yes; as long as the VCF is in spec and the variants have the annotations needed for the filter, VariantFiltration doesn’t know or care about the origin of the VCF or its variants.
I hope this helps! Please let me know if this information leads you to success. Thank you again for your patience and valued contribution to the GATK community. If you find any other questions arise in the future, please do not hesitate to reach back out.
Best,
Anthony -
Hi rohit satyam,
We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!
Kind regards,
Anthony
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