abyssum
commented
5 months ago Hello @renyuan001,
First of all, thank you for using NeoFuse.
To briefly answer your question, since GRCh38 (hg38) is and update of GRCh37 (hg19), there are several thousand individual bases updated in GRCh38, many of which corrected errors in coding sequences. Since this is beyond the scope of NeoFuse, I will not elaborate on the differences between the two versions (there is plenty of information available, this publication for example).
Although, I haven't tried to compare the results from the two versions myself, I would expect that you would find major differences between GRCh37 and GRCh38 as you mentioned (especially when it comes to genomic positions). As a quick example, consider BRCA2:
- According to GRCh37 the genomic coords of the coding positions for BRCA2 are as follows: chr13:32,890,598-32,972,907
- According to GRCh38 the genomic coords of the coding positions for BRCA2 are as follows: chr13:32,315,086-32,400,268
Following the previous example, let's say that the majority of the sequenced reads of your sample fall under the genomic position chr13: 32,315,086-32,400,268. Then depending on the annotation you would be using, BRCA2 may be called (using GRCh38) or not (when using GRCh37).
Given the fact that in order for Arriba to call a fusion the reads should span the junction point (for more info please read the arriba documentation regarding split reads, discordant mates and coverage), it is expected that since GRCh38 is more robust it will - probably - yield less results (meaning that GRCh37 might yield more results which are potentially false positives).
I hope this helps.
renyuan001
I use 10 samples and analysed both by GRCH37 and GRCH38. I conpared the ***filtered.tsv and unfiltered.tsv between GRCH37 and GRCH38. The fusion genes and locations were all different. No same result were found and it seems like the result referenced by GRCH38 was much fewer than the result referenced by GRCH37. Please tell me the reason， thank you! $ NeoFuse -R -o GRCH37 -n 20 -V GRCH37 --docker $ NeoFuse -R -o GRCH38 -n 20 -V GRCH38 --docker These orders were used to generate reference.