How to apply VQSR to mouse samples, to find the best thresholds for hard-filtering
REQUIRED for all errors and issues:
a) GATK version used: 4.4.0.0
b) Exact command used:
c) Entire program log:
gatk VariantRecalibrator \ -R Homo_sapiens_assembly38.fasta \ -V input.vcf.gz \ --resource hapmap,known=false,training=true,truth=true,prior=15.0:hapmap_3.3.hg38.sites.vcf.gz \ --resource omni,known=false,training=true,truth=false,prior=12.0:1000G_omni2.5.hg38.sites.vcf.gz \ --resource 1000G,known=false,training=true,truth=false,prior=10.0:1000G_phase1.snps.high_confidence.hg38.vcf.gz \ --resource dbsnp,known=true,training=false,truth=false,prior=2.0:Homo_sapiens_assembly38.dbsnp138.vcf.gz \ -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR \ -mode SNP \ -O output.recal \ --tranches-file output.tranches \ --rscript-file output.plots.R
I would like to adapt this command to my mouse samples. However, where could I find the vcf.gz files used in the "-resource" for this organism?
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Your best bet would always be the MGI database and Ensembl
https://www.jax.org/research-and-faculty/resources/mgi-snp-database
https://www.ensembl.org/Mus_musculus/Info/Index
You may also want to check the mouse genome project website for any additional resources
https://www.sanger.ac.uk/data/mouse-genomes-project/
I hope these would help.
Regards.
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Thank you for your response, I believe I will use resources from all the references you provided. However, how would I create the code? For example, instead of hapmap what would I put, would I change Known, or training, or truth, or prior parameters?
hapmap,known=false,training=true,truth=true,prior=15.0:hapmap_3.3.hg38.sites.vcf.gz
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Definition for this parameter indicates that prior values are not used by the algorithm therefore it may not be too crucial.
--resource <FeatureInput> A list of sites for which to apply a prior probability of being correct but which aren't
used by the algorithm (training and truth sets are required to run) This argument must be
specified at least once. Required.I will ask our team to get more insights into this matter.
Regards.
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Thank you very much for your availability.
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