Dear all,

I used Pindel v 0.2.4d for calling structural variants. I tried to convert the output to vcf with the following command:

pindel2vcf -p sample_pindel_chr6_D -r mouse_mm10.fa -R mm10 -d date

Unfortunately are lots of "N" in the allele and reference columns in the vcf file:

chr6    3314749 .       NN      N       .       PASS    END=3314751;HOMLEN=9;HOMSEQ=NNNNNNNNN;SVLEN=-1;SVTYPE=DEL       GT:DP   0/1:3
chr6    4756422 .       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN N       .       PASS    END=4756477;HOMLEN=8;HOMSEQ=NNNNNNNN;SVLEN=-54;SVTYPE=DEL       GT:DP   0/1:4
chr6    4758723 .       AT      A       .       PASS    END=4758725;HOMLEN=9;HOMSEQ=TTTTTTTTT;SVLEN=-1;SVTYPE=DEL       GT:DP   0/1:5
chr6    5057668 .       TNN     T       .       PASS    END=5057671;HOMLEN=29;HOMSEQ=NNNNNNNNNNNNNNNNNNNNNNNNNNNNN;SVLEN=-2;SVTYPE=DEL  GT:DP   0/1:3
chr6    6025302 .       TG      T       .       PASS    END=6025304;HOMLEN=10;HOMSEQ=GGGGGGGGGG;SVLEN=-1;SVTYPE=DEL     GT:DP   0/1:3
chr6    6114202 .       TA      T       .       PASS    END=6114204;HOMLEN=12;HOMSEQ=AAAAAAAAAAAA;SVLEN=-1;SVTYPE=DEL   GT:DP   0/1:3
chr6    6115137 .       GA      G       .       PASS    END=6115139;HOMLEN=10;HOMSEQ=AAAAAAAAAA;SVLEN=-1;SVTYPE=DEL     GT:DP   0/1:4
chr6    6329713 .       GT      G       .       PASS    END=6329715;HOMLEN=17;HOMSEQ=TTTTTTTTTTTTTTTTT;SVLEN=-1;SVTYPE=DEL      GT:DP   0/1:4
chr6    7819071 .       TA      T       .       PASS    END=7819073;HOMLEN=13;HOMSEQ=AAAAAAAAAAAAA;SVLEN=-1;SVTYPE=DEL  GT:DP   0/1:5
chr6    8175131 .       GAT     G       .       PASS    END=8175134;HOMLEN=16;HOMSEQ=ATATATATATATATAT;SVLEN=-2;SVTYPE=DEL       GT:DP   0/1:13
chr6    8187157 .       NNN     N       .       PASS    END=8187160;HOMLEN=17;HOMSEQ=NNNNNNNNNNNNNNNNN;SVLEN=-2;SVTYPE=DEL      GT:DP   0/1:3
chr6    8658349 .       NN      N       .       PASS    END=8658351;HOMLEN=12;HOMSEQ=NNNNNNNNNNNN;SVLEN=-1;SVTYPE=DEL   GT:DP   0/1:3

What could be the problem?

Best wishes