Dear all, I need help from anyone who has ever used ASCETS (https://github.com/beroukhim-lab/ascets) with WGS data. ASCETS produces arm-level copy-number variant calls and arm-level weighted average log2 segment means from segmented copy number data, and it calculates the aneuploidy score, which is what I am interested in. To do this, it uses a segmentation file that I obtained using Purple via nf-core oncoanlyser pipeline. This segmentation file requires to have the following columns:

sample

,

chromosome

,

segment start

,

segment end

,

number of markers

, and

log2ratio

(no need to use the same names) This is where my doubt arises: in my Purple segmentation file, I have the following columns, none of which seem equivalent to the number of markers or log2ratio: >

chromosome, start, end, germlineStatus, bafCount, observedBAF, minorAlleleCopyNumber, minorAlleleCopyNumberDeviation, observedTumorRatio, observedNormalRatio, unnormalisedObservedNormalRatio, majorAlleleCopyNumber, majorAlleleCopyNumberDeviation, deviationPenalty, tumorCopyNumber, fittedTumorCopyNumber, fittedBAF, refNormalisedCopyNumber, ratioSupport, support, depthWindowCount, tumorBAF, gcContent, eventPenalty, minStart, maxStart.

To clarify,

number of markers

column defined in ASCETS seems to be the per-segment count of probes/targets used to define that CNV segment, and the

log2ratio

is the segment’s copy-number signal expressed as a log base 2 ratio. From my understanding, the

log2ratio

column could be inferred using

log_2((minorAlleleCopyNumber} + majorAlleleCopyNumber})/2)

, but I could not find this in any of the Purple output files, or any way to estimate this directly from Purple output. Since Purple utilizes information from AMBER, I thought I could extract this value from there, but I could neither find it in the output. In AMBER documentation, it explicitly states the following: > "The loci file used by HMF for both the 37 and 38 reference genomes is available to download from HMF-Pipeline-Resources. These loci are generated using gnomAD v3 SNP sites (lifted over for the GRCh37 version) from chr1-chrX with only a single ALT at that location and with a population AF > 0.05 and < 0.95. These sites are further filtered to remove loci with frequently unclear zygosity in a set of 60 HMF samples, yielding around 6.3M sites overall." My idea was to download this file from the HMF Pipeline Resources and then infer how many SNPs fall within each of my segments. However, I couldn't find this file in the resources... Could anyone help me locate it, or does anyone have a better solution for obtaining the number of markers directly from Purple? Thanks in advance for your help

Hi, @Elisabet Figuerola! Slack uses channels to organise discussions. Press the

...

more option on the left sidebar. Then hover over Your organisation, and finally select Channels to browse. Each nf-core pipeline has it’s own channel (e.g. #CE8SSJV3N). Please post any questions about specific pipelines in the relevant channel. If you’re not sure where to post your message, please ask @Igor Trujnara for help.

thanks @Igor Trujnara, I'll forward the message there!