VCF parsing error - float instead of int

Hail Query & hailctl
1

Can I specify not to parse the culprit field (DP_MEDIAN) at all? or even not to parse the info field at all? or to parse it as a float?

Thanks!

The error is :
…
VCFParseError: invalid character ‘.’ in integer literal

EDIAN=131;GQ_MEDIAN=164;DP_MEDIAN=24.5;DP_HIST_ALT=52|201|434|701|671|63 …
^

‘info’: struct {
FS: array,
HOM: int32,
GC: array,
AD: array,
ADF: array,
ADR: array,
DP: int32,
MQ: int32,
DPF: int32,
AC: array,
AN: int32,
GQX_MEDIAN: array,
GQ_MEDIAN: array,
DP_MEDIAN: array,
DP_HIST_ALT: array

2

I think the core problem is that the header is wrong. You can either edit the header to indicate that DP_MEDIAN is a float, or if the VCF is large, extract the header alone, edit it, and use that in import_vcf with the header_file argument.

3

Thanks! header_file seems to work, still parsing and writing.