Closed d-henness closed 2 years ago
It seems that the algorithm used to generate the contig string can produce contigs not found in context83. This is a maf file that reproduces this error when using cosmic3_ID as the reference.
Chromosome | Start_Position | Variant_Type | Reference_Allele | Tumor_Seq_Allele2 | Tumor_Sample_Barcode |
---|---|---|---|---|---|
chr10 | 15119471 | DEL | TA | - | MF12 |
Hi @d-henness Sorry we missed this. As the error suggest, one of your mutations is labeled as a DSB despite being GC > GG which is a single base substitution instead. The Indel error occurs because your mutation is not left aligned. Looking at the sequence, we see that the reference is TTGATATCTTT
and your MAF shows a deletion of TA. That means the read had the sequence TTGATCTTT
. A left-aligned annotation would actually indicate a deletion of AT
from position 15119470. These two mutations are parsimonious, but the AT
deletion would be left-aligned. Hope this helps for any issues in the future.
Best regards, Yo Akiyama
Thanks for your reply @yoakiyama. Can you recommend any tools that will convert mutations into their left aligned forms? Also I had a look though the documentation for SignatureAnalyzer and didn't notice this requirement anywhere. It should be stated somewhere if this is a requirement.
I'm getting an error when running signatureanalyzer with the cosmic3_ID reference. The full command I run is
signatureanalyzer -n 10 --reference cosmic3_ID --hg_build /data/shared/hg38/hg38.2bit --objective poisson --max_iter 50000 --prior_on_H L1 --prior_on_W L1 -o cosmic3_ID all.maf
The error message is
I get a similar error when using cosmic_DBS as the reference