ACMG_class

[dbhayal9]

Hi,

I am running AnnotSV using the input from ExomDepth tool for CNA annotation. and i successfully executed command and interpreted results from output file using Scoring_Criteria_AnnotSV_latest.xlsx file.

AnnotSV worked for both type of annotation CNA and SV?

also a column from output file have 2 type classes 1 and full=1 or 5 and full=5 so what is diffirent between them?
ACMG_class
4
1
4
4
4
4
full=5
full=3
full=1
full=5
full=3
full=5
full=5
full=5
full=5

Thanks in advance.

[lgmgeo]

Two types of lines are produced by AnnotSV (cf the “AnnotSV type” output column):

• An annotation on the “full” length of the SV:
  Every SV are reported, even those not covering a gene. This type of annotation gives an estimate of the SV event itself.
• An annotation of the SV “split” by gene:
  This type of annotation gives an opportunity to focus on each gene overlapped by the SV. Thus, when a SV spans over several genes, the output will contain as many annotations lines as covered genes (cf example in FAQ of the README)

In the ACMG_class annotation column, you have the values :

• 1, 2, 3, 4, 5 or NA for each "full" line.
• full=1, full=2, full=3, full=4, full=5, full=NA for each "split" line (reports the ACMG_class value of the corresponding full line)

Warning:
SV ranking is only available for GAIN (duplications) and LOSS (deletions). And therefore, only available when the
SV type is known (The -svtBEDcol option is required when the SV input file is a BED). If not available, the “NA”
value is attributed (Non Attributed). INS are not yet ranked.