anleopa

Hi @rkimoakbioinformatics, A locally installed OpenCRAVAT

Yes! I see it... some of them correspond to "Liftover failure" in the annotator and "syntax error" in the aggregator. What could be causing the "leftover failure"?

These are a some examples: SOURCE:error.aggregator LINE:0 INPUT:1 948846 T TA 0.41880342 0.41880342 049 p36.33 3 117 67,49,25,24 UPSTREAM(MODIFIER||||ISG15|mRNA|CODING|NM_005101|) (NC_000001.10:g.948846_948847insA,NM_005101.3:c.-108_-107insA,) . 36 OMIM:147571 0 117,0,49,0 HET 1.0E-25 ERROR:near "(": syntax...

In the case of liftover failures... for example, in this record the variant is located in chr1 pos 145558565 (GRCh37) C>G This variant has GRCh38 coordinates: 145,876,516 as can be...

This is what I have found in the log file: 2022/01/26 11:14:07 cravat.aggregator Traceback (most recent call last): File "C:\Program Files (x86)\open-cravat\python-3.7.2.amd64\lib\site-packages\cravat\aggregator.py", line 154, in run self.cursor.execute(update_template, ins_vals) sqlite3.OperationalError: near...

I have also found that in some cases the ref and al alleles change between assemblies. For example, rs67270413 is G>A in GRCh37 and A>G in GRCh38. In this case,...

Yes, you are right about the INFO fields... This is the output of a pipeline, but I don't have the details about the technology/software used... I can try to find...

> > I have also found that in some cases the ref and al alleles change between assemblies. For example, rs67270413 is G>A in GRCh37 and A>G in GRCh38. In...

> > Yes, you are right about the INFO fields... This is the output of a pipeline, but I don't have the details about the technology/software used... I can try...

I was thinking about SNPs and small indels