Comments (3)
ACEnglish
commented on June 24, 2024
The GM128*.vcf has a header definition of ID=SVTYPE,Number=A. This is causing Truvari to see its svtype as a tuple e.g. ("INS",) instead of string "INS". By changing the header line to:
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Variant type">
I was able to see:
{
"TP-base": 18,
"TP-call": 18,
"FP": 1,
"FN": 25,
"precision": 0.9473684210526315,
"recall": 0.4186046511627907,
"f1": 0.5806451612903226,
"base cnt": 43,
"call cnt": 19,
"TP-call_TP-gt": 0,
"TP-call_FP-gt": 18,
"TP-base_TP-gt": 0,
"TP-base_FP-gt": 18,
"gt_concordance": 0.0,
"gt_matrix": {
"(1, 1)": {
"(None, None)": 6
},
"(1, 0)": {
"(None, None)": 3
},
"(0, 1)": {
"(None, None)": 9
}
}
}
Truvari uses pysam to parse VCF files and while there are safe guards for Number=. (See line) I'll need to edit that line for Number=A and others which tell pysam to return tuples instead of lists via:
if isinstance(ret_type, (list, tuple)):
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ACEnglish
commented on June 24, 2024
Sorry, one more thing... The --giabreport can only be used on the GIAB vcfs. See wiki
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zhengdafangyuan
commented on June 24, 2024
Thanks, I followed the step you mentioned and it worked.
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