Guidance on RNA-Seq / Tumor Data

[sstadick]

Hello!

In your paper you mention that:

There are other possible useful extensions to our joint contamination and estimation method. We are extending these methods to detect and estimate contamination for RNA-seq and other epigenomic sequence data. The method can also be extended to handle contamination in cancer genomic data.

Do you have any guidance or suggestions on how to run verifybamid2 in either of those scenarios?

[hyunminkang]

For RNA-seq, if you run it as if it is an exome sequence data, it should work reasonably well. For other omics data, you just need to change the regions to focus on the regions you expect. There are room for optimization, but should run well out of the box. Hyun. ----------------------------------------------------- Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

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On Tue, Sep 22, 2020 at 5:29 PM Seth ***@***.***> wrote: Hello! In your paper you mention that: There are other possible useful extensions to our joint contamination and estimation method. We are extending these methods to detect and estimate contamination for RNA-seq and other epigenomic sequence data. The method can also be extended to handle contamination in cancer genomic data. Do you have any guidance or suggestions on how to run verifybamid2 in either of those scenarios? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#20>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABPY5OLSYYZR7MXIDJDVOHDSHEJL3ANCNFSM4RWIQ6PQ> .

[nh13]

@hyunminkang how about for somatic data, where we do not expect heterozygous sites to have 50% allele frequency. In the previous version of verifyBamId, we could input the called genotypes.

[hyunminkang]

verifyBamID2 does not (yet) have a routine to check with genotypes unfortunately. You can still use verifyBamID1 to perform such analysis. Hyun. ----------------------------------------------------- Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

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On Tue, Sep 22, 2020 at 6:33 PM Nils Homer ***@***.***> wrote: @hyunminkang <https://github.com/hyunminkang> how about for somatic data, where we do not expect heterozygous sites to have 50% allele frequency. In the previous version of verifyBamId, we could input the called genotypes. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#20 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABPY5OLEQR6MGPXLZ2N62ADSHEQ4NANCNFSM4RWIQ6PQ> .

[sstadick]

@hyunminkang thanks for taking the time to respond! I will use verifyBamID1 for now for somatic data.