Entering edit mode
13 months ago
yixing
•
0
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
