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ShixiangWang / DoAbsolute

:package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package
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to analyze purities using panel sequencing data #30

Closed h170607 closed 1 year ago

h170607 commented 1 year ago

Hi, @ShixiangWang We want to analyze the purity and ploidy of a set of tumor samples using panel sequencing data (over 700 genes). The segment files were from CNVkit and maf files were from Mutect2 and vcf2maf. We are not sure if the platform parameter should use "SNP_6" or "Illumina_WES". Tried both options, and we found that several samples were 1 or 0.99 pure, ploidy was irregular, but some were above 7. Does this mean that some parameters are not suitable? In addition, some purity results are quite different from those calculated by other software. Is this normal?

best, Matt

ShixiangWang commented 1 year ago

For panel sequencing, I recommend you use the Sequenza or the latest version of ASCAT.

h170607 commented 1 year ago

Thanks for your reply. Do you mean that absolute and DoAbsolute are mainly suitable for analyzing wes and wgs data? In addition, it seems that the broadinstitute no longer supports absolute, and the document and download links on genepattern is also invalid. Will this affect the subsequent use of absolute and DoAbsolute?

ShixiangWang commented 1 year ago

Yes. The ABSOLUTE did not say that it could handle target sequencing data, so I don't recommend it.

The use of DoAbsolute is not affected.

h170607 commented 1 year ago

Could you please share the document of absolute mentioned in https://www.jianshu.com/p/468077752689, since the official link is invalid?

ShixiangWang commented 1 year ago

No. I haven't backup. I found only the link https://www.genepattern.org/analyzing-absolute-data#gsc.tab=0 works.

h170607 commented 1 year ago

Thanks a lot