Question: InterVar and Varsome discrepancies in ACMG classification
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gravatar for cocchi.e89
10 days ago by
cocchi.e8920
cocchi.e8920 wrote:

I am working on ACMG classification of variants in a cohort of patients, I found that InterVar classification differs (generally more strict for what does it seems to me at the moment) form Varsome, e.g. var X-107939570-C-T is classified as "Pathogenic" by Varsome (https://varsome.com/variant/hg19/X-107939570-C-T) and Uncertain Significance by InterVar (command line tool: "InterVar: Uncertain significance PVS1=0 PS=[0, 0, 0, 0, 0] PM=[0, 1, 0, 0, 0, 0, 0] PP=[0, 0, 1, 0, 1, 0] BA1=0 BS=[0, 0, 0, 0, 0] BP=[0, 0, 0, 0, 0, 0, 0, 0]")

At the same manner var: X-107898624-G-T. Varsome: Likely Pathogenic (https://varsome.com/variant/hg19/X-107898624-G-T) and Intervar: "InterVar: Uncertain significance PVS1=0 PS=[0, 0, 0, 0, 0] PM=[0, 1, 0, 0, 0, 0, 0] PP=[0, 0, 1, 0, 1, 0] BA1=0 BS=[0, 0, 0, 0, 0] BP=[1, 0, 0, 0, 0, 0, 0, 0]"

Does somebody has got a clue for this difference? There are other command line tools to make this annotation automated (make more similar to Varsome "relaxed" interpretation?

Thanks a lot in advance for any help!

ADD COMMENTlink modified 5 days ago by zankov0 • written 10 days ago by cocchi.e8920

Hey I am also working on ACMG classification and was wondering what command you used with InterVar and also how your vcf is structured since I am struggling to get an output in general.

Thanks in advance for your help!

ADD REPLYlink written 5 days ago by zankov0

Just clone the InterVar repo on GitHub:

git clone https://github.com/WGLab/InterVar.git

and then access the InterVar directory in which you find the python script InterVar.py Call it on a normal VCF file with, as example (I use python3.7 but any distribution >3.3 should work properly):

python3.7 InterVar.py  \
    -b hg19 \
    -i <your_input.vcf> \
     --input_type=VCF \
     -o <your_output>

And then you will find your output files where you specified. Please note, in the same InterVar directory you must download Annovar executables (annotate_variation.pl, convert2annovar.pl, retrieve_seq_from_fasta.pl, coding_change.pl, table_annovar.pl, variants_reduction.pl) and the first time you run it will take long in order for Annovar to download all its reference databases in the "humandb" directory that will appear in the same "InterVar" directory where you launch the script.

ADD REPLYlink modified 5 days ago • written 5 days ago by cocchi.e8920
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