Error in if (nMinor < 0) { : missing value where TRUE/FALSE needed Calls: callSubclones -> determine_copynumber

[wedge-lab]

Error in if (nMinor < 0) { : missing value where TRUE/FALSE needed Calls: callSubclones -> determine_copynumber

[sdentro]

Thanks for reporting this issue and many thanks for the fix @lydiayliu ! Closing this ticket now.

[Sames-Jtudd]

I have the same error. The error orginated in the follwing line of the command Battenberg:::determine_copynumber
33 nMinor = (rho - 1 + (1 - l) * psi * 2^(LogR/gamma))/rho

the reason was that l was "NA". l is derived from the BAFsegment file segment column, which were all NA in my case. Not sure why. If you figure it out let me know.

[keiranmraine]

We see this frequently and abandon the analysis of these samples. It would be useful if there was an appropriate error message indicating the cause of this.

[lydiayliu]

I also ran into this issue with our bwa-mem2 aligned samples to GRCh38 that are of East Asian ancestry.

After following the line of inquiry given above, I confirmed that the error is due to l being NA in

nMinor = (rho - 1 + (1 - l) * psi * 2^(LogR/gamma))/rho

in Battenberg:::determine_copynumber.
This is due to the .BAFsegment. file containing NA for stretches of multiple chromosomes. Following this problem upstream I realized that in the _alleleFrequencies_chr files, the problematic regions have good depth = 0.

Further investigation revealed that the reason there is no depth in those regions is because the regions have ALT CONTIGS where all the reads were aligned to instead, resulting in depth = 0 in the alleleCounter result for the regions.

I'm trying to avoid the problematic regions (since they are very small anyways) by adding a check to skip the segment if nMinor is NA.

Update: was able to avoid this issue and skip the problematic short contigs with read depth of 0. In the determine_copynumber function, add

    if (is.na(nMinor)) {
        print('SKIPPING NA NMINOR')
        next
    }

before the problematic line

    # Increase nMajor and nMinor together, to avoid impossible combinations (with negative subclonal fractions)
    if (nMinor<0) {