Entering edit mode
9.8 years ago
d.esser
•
0
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
Are you using the same reference build to run Pindel2vcf? Can you update your pindel to the latest version?