Final autogvp output currently does not retain autopvs1 criterion column. Additionally, raw evidence columns (PVS1, PM, etc.) are being retained rather than corrected evidence columns. See example below, where all variants with criterion == "na" should have PVS1 == 0 in final output:
# A tibble: 17 × 3
vcf_id criterion evidencePVS1
<chr> <chr> <dbl>
1 1-236736564-C-T na 1
2 10-72204485-G-C na 1
3 11-47285079-C-T na 1
4 14-74296383-G-C na 1
5 15-82688452-CG-C na 1
6 16-58543411-GA-G na 1
7 16-89649432-G-A na 1
8 17-17221490-C-T na 1
9 17-63838627-G-A na 1
10 17-76291810-G-A na 1
11 4-1093699-G-A na 1
12 4-142028797-TC-T na 1
13 5-83353124-G-A na 1
14 6-41798694-C-CCCCCA na 1
15 6-47795559-C-CAA na 1
16 7-80671101-G-GA na 1
17 7-80672795-C-CA na 1
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Final autogvp output currently does not retain autopvs1
criterioncolumn. Additionally, raw evidence columns (PVS1, PM, etc.) are being retained rather than corrected evidence columns. See example below, where all variants withcriterion == "na"should havePVS1 == 0in final output:What version are you using?
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sessionInfo()and post the output below