Dear sir, I want to constract a graph pangenome.

 vg autoindex --threads 40 --workflow giraffe -T ./ -r line.fastaa -v combin.rename.re.vcf.gz -p 97samples.combined

But I found some warnings in the log. Are these warnings normal? These symbol(".") represents a deletion And how can I avoid them?

warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      3       .       CCC     .,ACC,CATCC,C   1723.58 .       AC=5,18,0,0;AF=0.055,0.198,0,0;AN=91;DP=2730;
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      4       .       C       .,CTACCC,T      1474.12 .       AC=2,17,0;AF=0.022,0.185,0;AN=92;DP=2760;MLEA
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      5       .       CTAAA   .,C     1323.14 .       AC=1,16;AF=0.011,0.174;AN=92;DP=2760;MLEAC=1,16;MLEAF
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      6       .       T       .,TTA,C,TCTCACAACAACAACGGAGGAGGAGG      1418.25 .       AC=3,16,0,0;AF=0.033,
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      7       .       AAACCCTAAACCTAAACCCTAAACCCTAAACCCTAAACCTAAACCCTAAACCCTAAACCTAAACCCTAAACCTAAACCCTAAACC
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      8       .       AA      .,AGA,A 1300.95 .       AC=2,15,0;AF=0.022,0.163,0;AN=92;DP=2760;MLEAC=0,8,8;
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      9       .       A       .,C     1323.17 .       AC=1,16;AF=0.011,0.174;AN=92;DP=2760;MLEAC=1,16;MLEAF
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      10      .       CCCTAAACCTA     .,ACCTAAACCTA,C 1271.76 .       AC=3,14,0;AF=0.033,0.152,0;AN=92;DP=2
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      11      .       CCTAA   .,C,TCTAA,GCTAA 1335.39 .       AC=3,15,0,0;AF=0.033,0.163,0,0;AN=92;DP=2760;
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      12      .       CTAAACCTAAACCCTAAACCCTAAACCCTAAACCTAAACCCTAAACCCTAAACCTAAACCCTAAACCTAAACCCTAAACCCTAAA
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      13      .       T       .,A,C,G 1551.43 .       AC=4,17,0,0;AF=0.043,0.185,0,0;AN=92;DP=2760;MLEAC=0,
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      14      .       A       .,C     1323.17 .       AC=1,16;AF=0.011,0.174;AN=92;DP=2760;MLEAC=1,16;MLEAF
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      15      .       AACCTAAACCCTAAACCCTAAACCCTAAACCTAAACCCTAAACCCTAAACCTAAACCCTAAACCTAAACCCTAAACCCTAAACCC
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      16      .       ACCTAA  .,A,CCCTAA,AACCCTAA,ATACCCTAA   1852.73 .       AC=12,16,0,0,0;AF=0.13,0.174,
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      17      .       CCTAA   .,C,GCTAA       1570.56 .       AC=2,18,0;AF=0.022,0.196,0;AN=92;DP=2760;MLEA
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      18      .       CTAAACCCTAAACCCTAAACCCTAAACCTAAACCCTAAACCCTAAACCTAAACCCTAAACCTAAACCCTAAACCCTAAACCCCTA
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      19      .       T       .,C,TT  1942.01 .       AC=5,21,0;AF=0.054,0.228,0;AN=92;DP=2760;MLEAC=0,6,20
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      20      .       A       .,C,T   1907.16 .       AC=4,21,0;AF=0.043,0.228,0;AN=92;DP=2760;MLEAC=0,18,7
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      21      .       AA      .,A,TA,CA       1857.96 .       AC=4,20,0,0;AF=0.043,0.217,0,0;AN=92;DP=2760;
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      22      .       A       .,AACCCAA,T     1653.55 .       AC=2,19,0;AF=0.022,0.207,0;AN=92;DP=2760;MLEA
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      24      .       C       .,A,T   1422.85 .       AC=3,16,0;AF=0.033,0.174,0;AN=92;DP=2760;MLEAC=0,7,12
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      25      .       C       .,T,CC,CAGACTGTGAG      1372.51 .       AC=4,15,0,0;AF=0.043,0.163,0,0;AN=92;
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      26      .       T       .,A     1235.52 .       AC=1,15;AF=0.011,0.163;AN=92;DP=2760;MLEAC=1,15;MLEAF
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      27      .       A       .,ATACCCTAAACCCT        1235.48 .       AC=1,15;AF=0.011,0.163;AN=92;DP=2760;
warning:[vg::Constructor] Variant with '.' among multiple alts being skipped: Chr3      28      .       A       .,T     1235.52 .       AC=1,15