Hi, I want to run PyClone analysis for a subset of the posted data. By the way, thank you for such an effort to put all this together. I do not know if I am missing something, red through the discussion and still do not get it. Please how do I get data for the PyClone input table **'ref_counts'** and** 'alt_counts'**, i.e. number of reads matching the reference allele and number of reads matching the alternate allele? Thanks ahead! Radka

Created by Radka Ptacnikova RadkaP
Hi Kevin, alright, I got you. Thanks for the explanation! Radka
Hi @RadkaP , You would look for overlaps between the larger TITAN segments and the passgeno genomic locations. In our internal database, we structure both of these as a variable called "pos" that has both the start and stop coordinates (e.g., "[70570290,70695983)" ) and we look for whether the "pos" overlaps between TITAN segments and passgeno. Please see the github page for the [query](https://github.com/fsvarn/GLASSx/blob/master/sql/pyclone/pyclone_create_tsv.sql) we use in constructing the pyclone tsv file. Note that this script is only meant to serve as a framework since our internal database structure differs from what's publicly available on Synapse. -Kevin
Hi Kevin, thanks for your reply. There I have been as well, that's the only place where these shortcuts occur, I have screened all tables. But in the table 'variants_titan_seg', where are values for 'copy_number', 'major_cn' and 'minor_cn', which values one also needs for the PyClone analysis, are between 'start' and 'end' relatively larger chunks of genome. Whereas in the 'varriants.passgeno' the values ad_ref and 'ad_alt' refer to one up to few nucleotide variants only. So how can be then the 'ad_ref' and 'ad_alt' from these short sequence variants applied for copy numbers? Thanks! Radka
Hi @RadkaP, Thanks for the recognizing the value of the resource. It sounds like the information you are looking for is located in the `variants.passgeno` table under Files where there is information on "ad_ref" and "ad_alt" (See data dictionary). Hope this helps, Kevin

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