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If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
GATK4.0.9.0 undetected a delins site
qiuqiu87
Member ❠
Dear GATK team,
I use GATK4.0.9.0 Haplotypercaller to detect germline variation, and find a delins site is not call. As the figure show, this is gvcf output, 32944606 is delTTT, and 32944609 is insAAAA. But the vcf output only is delTTT, insAAAA is filtered. And I find the in GATK4.1.1.0 and 4.1.2.0 also not call insAAAA in vcf. The site is verified by Sanger, and is a delinsAAAA. So why GATK4.0.9.0 filtered the insAAAA in 32944609 ?
The vcf of GATK4.0.9.0:
chr13 32944606 . CTTT C 9318.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.294;DP=814;ExcessHet=3.0103;FS=1.093;MLEAC=1;MLEAF=0.500;MQ=60.03;MQRankSum=0.000;QD=11.90;ReadPosRankSum=0.290;SOR=0.769 GT:AD:DP:GQ:PL 0/1:423,360:783:99:9326,0,45236
I use GATK4.0.9.0 Haplotypercaller to detect germline variation, and find a delins site is not call. As the figure show, this is gvcf output, 32944606 is delTTT, and 32944609 is insAAAA. But the vcf output only is delTTT, insAAAA is filtered. And I find the in GATK4.1.1.0 and 4.1.2.0 also not call insAAAA in vcf. The site is verified by Sanger, and is a delinsAAAA. So why GATK4.0.9.0 filtered the insAAAA in 32944609 ?
The vcf of GATK4.0.9.0:
chr13 32944606 . CTTT C 9318.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.294;DP=814;ExcessHet=3.0103;FS=1.093;MLEAC=1;MLEAF=0.500;MQ=60.03;MQRankSum=0.000;QD=11.90;ReadPosRankSum=0.290;SOR=0.769 GT:AD:DP:GQ:PL 0/1:423,360:783:99:9326,0,45236
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Answers
Hi @qiuqiu87,
"HaplotypeCaller performs a local reassembly and realignment of the reads in the region surrounding potential variant sites" then the tool calls the variants. If you would like to know more about how haplotypecaller calls variants you can read through Local re-assembly and haplotype determination.
The site in question may not have met the default threshold to be considered a variant by Haplotypecaller due to quality of evidence. However, the tool does have parameters that can be tweaked to be more sensitive to calling variants which can be found in the tool documentation page (warning, this increases the chance of false positives).
If you believe the tool is misbehaving please read the following doc Generate a "bamout file" showing how HaplotypeCaller has remapped sequence reads to generate a bamout and a IGV screenshot of the region not being called and post it here.
The screenshot showed the raw bam and bamout about the not being called region. The two bam files have reads support the variant.
I'll ask the dev team, in the meantime tell us more about the background. e.g. What's its origin (human, exome), what is the exact command you used, what was the sequencing platform, are you working with amplicon data?
Thanks for your answer. The command I used is the default command with -O to output vcf. The data is about human sequence, the tumor detection panel with amplicon data. And as I paste the gvcf output, the qual of 32944609 is 0, so is filtered before output vcf.
And I try some versions, and find 4.0.9.0 and higher version can't detect the insAAAA variants.
I've asked the dev team, I'll let you know what they say.
In the meantime let me know if using
--adaptive-pruningand--kmer-size 35as suggested in this forum post helpshttps://gatkforums.broadinstitute.org/gatk/discussion/comment/57464#Comment_57464
Then from this point the above message may apply
@qiuqiu87 Hi , have you solved your questions ?
@bshifaw Hi , what's going on about this missing complex mutations ?
Hi ,
The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.
Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.
We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.
For context, see this [announcement](https://software.broadinstitute.org/gatk/blog?id=24419 “announcement”) and check out our [support policy](https://gatkforums.broadinstitute.org/gatk/discussion/24417/what-types-of-questions-will-the-gatk-frontline-team-answer/p1?new=1 “support policy”).