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how can vqsr applied on small data set?

ying_sheng_1ying_sheng_1 Posts: 49Member
edited September 2012 in Ask the GATK team

We have data from target sequencing genes (only targeted two genes). We analyzed the data by GATK pipeline. Since the data set is too small, we tried hard filtration on both SNP and indels. At the same time, we sequenced the same sample by whole exome sequencing and filter SNP by VQSR. The quality of VQSR results is much better than hard filtration results. For economic reason, we need to develop analysis pipeline for target sequencing, is it ok to incorporate the target sequencing data into an exome sequencing data (merge the VCF files), do VQSR? I just worried the true sites in target sequencing data have different features compared to true sites in whole exome sequencing data.

Post edited by Geraldine_VdAuwera on

Best Answer

  • rpoplinrpoplin Posts: 122GATK Dev mod
    Answer ✓

    Hi there,

    This is a great idea and I would imagine that it might work well. It really depends on, as you say, the differences between the characteristics of the exome targeted sequencing and the small target sequencing. Perhaps one thing you can do to convince yourself that this is working is to create a plot of the VCF annotation distributions for the two data types. Hopefully the distributions will lie on top of each other.

    Cheers,

Answers

  • rpoplinrpoplin Posts: 122GATK Dev mod
    Answer ✓

    Hi there,

    This is a great idea and I would imagine that it might work well. It really depends on, as you say, the differences between the characteristics of the exome targeted sequencing and the small target sequencing. Perhaps one thing you can do to convince yourself that this is working is to create a plot of the VCF annotation distributions for the two data types. Hopefully the distributions will lie on top of each other.

    Cheers,

  • ying_sheng_1ying_sheng_1 Posts: 49Member

    Thanks! I will try this out and share the results here.

  • ying_sheng_1ying_sheng_1 Posts: 49Member

    I have checked the feature distributions. The features for target sequencing set are different from those of exome sequencing. I combined vcf files from 84 samples, the VQSR goes through. However, the target sequencing samples are captured by Halo technology (DNA is shearing by restriction site, in stead of random shearing), I expect the features recommended for exome sequencing might not be applicable for Halo capture. Could you share the experience for how to find the best feature set for training the model? Thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,760Administrator, GATK Dev admin

    For now, the best resource for you to look at is the "non-human data" FAQ in this article:

    http://www.broadinstitute.org/gatk/guide/article?id=39

    We will try to put together some more detailed recommendations in the near future, but I can't promise you when that will get done, sorry.

    Geraldine Van der Auwera, PhD

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