Deleted and inserted sequence and inserting position related to VARPOS in VAR file

[Former user]

Hi Charlie,

I have a question on the actual deleted and inserted sequence related to the VARPOS provided in VAR file.

For the example of a DEL in VAR file, the actual deleted sequence I found is at chr1:1454002-1455001. However, this DEL recored in output bed file as chr1:1454000-1455000. #VID MID VARFREQ VARHAP VARCHR VARPOS VARDEL VARDELSIZE VARINS VARINSSEQ(HAP/SEQFILE,CHR:START-END,COPY,REVCOMP) VAR_1 DEL_1 1.0 0 1 1454000 True 1000 False None

For the example of DUP in VAR file, the actual deleted sequence is at chr2:1870002-1871001 and inserted sequence is same as in VAR file (chr2:1870001-1871000). In addition, the inserted sequence is inserted after the base 1870001, which duplicated one base (1870001) and cause one base deleted (1871001). VAR_41 DUP_1 0.5 0 2 1870000 True 1000 True example.fna,2:1870001-1871000,2,f

Could you help me with this problem? Are there anything I missed in VAR file?

Thank you for the help.

[Charlie Xia]

Emm, I will check when I got time.

Likely one base diff somewhere in the code.

If you can come up with some fix, greatly appreciated!