Closed kw10 closed 1 year ago
Hi @kw10,
When you say 'sites', you mean 'SNPs', right? If that's the case, then we don't have any built-in function to do that but this should be very straightforward. One can iterate on each segment (ascat.output$segments
) and count how many SNPs are located within such regions (ascat.bc$SNPpos
). Because ASCAT relies on heterozygous SNPs to derive allele-specific profiles, I would also count the number of hetSNP per segment (check ascat.bc$Tumor_BAF_segmented
).
Cheers,
Tom.
Hi Tom,
Thanks for your response. Yes, I mean SNPs. A follow-up question - if I used a BED file (I have exome data), should I count only the SNPs that fell within the BED regions?
Thanks again, Kim
Hi @kw10,
You can, all SNPs outside of the BED definition would have been discarded anyway.
Cheers,
Tom.
Ah, right! Thanks!
Hello,
Is there a way to determine the number of sites that were considered for each segment that is present in the *segments.txt file? I am running
ascat.prepareHTS
using tumour and normal BAM (exomes) and using the recommended files downloaded from the Battenberg github repository.Thanks Kim