Failed on the variants calling with low quality pacbio seq

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Lei Xu

• May 12, 2021 11:47

Hi,

I tried to variants calling with GATK on my pacbio seq data. 

the base quality is low. I called with 

/data/software/gatk-4.1.8.1/gatk HaplotypeCaller --base-quality-score-threshold 6 --min-base-quality-score 0 --minimum-mapping-quality 0 -R $ref -I ${outdir}/${base}_sorted_dedup.bam -O ${outdir}/${base}_sorted_dedup.bam.vcf

I know the parameter setting is too low, but the vcf out put file is still empty. 

May I ask which parameter can set the minimum reads of the variant allele base? 

I can get the variants calling with deepvirant software with setting the o base quality and minimun reads of variant allele base. I did not find a solution with GATK. Thank you very much.

Best,

Lei

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  Genevieve Brandt (she/her)

  • May 27, 2021 16:14

  Hi Lei Xu, 

  Are you able to run BQSR (Base Quality Score Recalibration)? Here is some information about that step, it might help with your use of GATK: https://gatk.broadinstitute.org/hc/en-us/articles/360035890531-Base-Quality-Score-Recalibration-BQSR-

  We really don't recommend new users to use advanced parameters because the results will not be good quality. You could try disabling the read filters, but like I said, we don't recommend doing that and we cannot guarantee good results after disabling read filters.

  Here is another post where a user had a question about using GATK with PacBio reads: https://gatk.broadinstitute.org/hc/en-us/community/posts/360072716972-Variant-calling-with-PacBio-HiFi-reads. There are long reads pipelines that has been in development by our team which could also be helpful: https://dockstore.org/search?search=long-read-pipelines

  Have other users come across this same issue? How did you solve it with GATK?

  Best,

  Genevieve

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