Philippe Sanio

Hi @adbeggs Which install did you use for Spectre pip or the local installation? This issue has been fixed two commits ago (0e96275) and is already part of the local...

Hi @adbeggs Just wanted to check if the new Spectre version 0.2.1 fixed your issues? Cheers, Philippe

Hello @EugeneKim76 Thank you! **Short answer**: Yes, you can adjust the minimum CNV length from 100kb as low as 10kb, with the drawbacks of introducing false positives (FPs). **Long answer**:...

Hi @pcr876 This seems to be caused by the `--only-chr chr1,2,5,6,7,9,10,15,17,19,X` statement. You did it correctly for chromosome 1 with chr1. However, this has to be the same for the...

Hello @EugeneKim76 This can very well be a normal behavior of Spectre compared to qdnaseq. Could you please be so kind and provide me the command you used for running...

Hi @EugeneKim76, Thank you for providing more details. Which version of Spectre are you running? I see a couple of old flags in your **command which are not present in...

Hi @SergeWielhouwer > Using mosdepth I tried to create required regions.bed.gz file for use with Spectre, which worked fine with the following: mosdepth -t {threads} -x -b 1000 -Q 20...

Hi @bartcharbon Yes, you can use this reference in combination with the GRCh38 blacklist. All the blacklists we provide are based on the UCSC genome browser gap data. However, the...

Hi @adbeggs The duplication looks fairly obvious to me. However, it is just 4kb in size, which is outside the scope of Spectre. Spectre was designed to detect large CNVs...

Hi @TrentPrall Thank you! The `regions.bed.gz` file originates from Mosdepth, and the last column represents the read depth per bin (e.g. 1kb). The last column in the output file `cnv.bed.gz`...