Comments (3)
I am also hitting this problem. Entries in the VCF you output have non-ascii characters. Here is an example VCF entry:
6 26555722 6_25759412-26580983_2 T <DEL> . PASS SV_TYPE=DEL;END=26555744;CI_POS=-7,7;CI_END=-7,7;SR=1;PE=2;SV_SPAN=22;EVENT\ _SPAN=41357;EVENT_START=26514387;EVENT_END=26555743;EVENT_AFFECTED_LEN=69;EVENT_NUM_SV=2;REF_STRUCTURE=ABCDE;ALT_STRUCTURE=ABBBCE;SEGMENT_ENDPTS=25759412,2\ 6514387,26514434,26555722,26555744,26580984;SEGMENT_ENDPTS_CIWIDTH=0,9,12,14,14,0;AF=0.500;SCORE_VS_REF=235.57;SCORE_VS_NEXT=0.33;NEXT_BEST_STRUCTURE=ABCDE\ FGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz{||}~^?\200\201\202\203\204\205\206\207\210\211\213\214\215\216\217\220\221/ABCDEFGHIJKLMNOPQRSTUVWXYZabcdef\ ghijklmnopqrstuvwxyz{|}~^?\200\201\202\203\204\205\206\207\210\211\212\213\214\215\216\217\220\221;NUM_PATHS=448 GT 1/0
The string "^?\200\201\202\203\204\205\206\207\210\211\213\214\215\216\217\220\221" appears as a space in editors that can handle the mixed encodings. HOWEVER, this is a serious problem as standard VCF parsers all choke on these entries. For the moment I have to throw away these calls to use the rest of the data, not an ideal situation.
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