ERROR: [ERROR] Input string for the chromosomal change

[zillurbmb51]

Hello, I was trying to annotate a 6 column bim file using jannovar:

jannovar annotate-csv -d data/hg38_ensembl.ser -i merged.plink.bim -c1 -p 4 -r 5 -a
 6 --header --type TDF

I am getting this:

INFO Deserialization took 7.31 sec.
1       .       0       14464   A       T       HGVS    FunctionalClass
ERROR: [ERROR] Input string for the chromosomal change 1:14542A>G does not fit the regular expression ... :(
de.charite.compbio.jannovar.JannovarException: [ERROR] Input string for the chromosomal change 1:14542A>G does not fit the regular expression ... :(

Annotation of corresponding vcf works without error against same database. Any Help? Best, Zillur

[holtgrewe]

Hi, the regular expression is

		Pattern pat = Pattern.compile("(chr[0-9MXY]+):([0-9]+)([ACGTN]*)>([ACGTN]*)");

which means it must start with chr...