clody23
commented
5 years ago Hi,
this issue should have been resolved by this latest fix: https://github.com/mitoNGS/MToolBox/commit/890ed0998a2440a3aedeb97d3c6461a633674c2a
Can you please update and rerun and let us know if this resolves your issue?
Many thanks.
Claudia
cefrnch
Hi,
With the newest version v1.2, some (but not all) multi-allelic sites in sample.vcf have have 'None' as the genotype as below:
chrMT 310 . T TC,C . PASS AC=1,1;AN=2 GT:DP:HF:CILOW:CIUP:SDP None:1492:1.0,0.193:0.997,0.169:1.0,0.22:36;1456,95;88
Position 310 has this problem in most of my samples, but it sometimes happens at other positions. Below is the beginning of a sample.vcf showing the issue. I'm currently getting around it by replacing 'None' with '.'
Thank you.
fileformat=VCFv4.0
reference=chrRCRS
FORMAT=
FORMAT=
FORMAT=
FORMAT=
FORMAT=
FORMAT=
INFO=
INFO=
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NGC00378_01_mito
chrMT 263 . A G . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:2596:0.999:0.997:1.0:973;1621 chrMT 299 . C CA . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:2246:0.005:0.003:0.009:11;0 chrMT 302 . A AC,C . PASS AC=1,1;AN=3 GT:DP:HF:CILOW:CIUP:SDP 0/1/2:829:0.101,0.017:0.083,0.01:0.124,0.028:72;12,1;13 chrMT 309 . C CCT . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1715:0.003:0.001:0.008:0;6 chrMT 310 . T TC,C . PASS AC=1,1;AN=2 GT:DP:HF:CILOW:CIUP:SDP None:1492:1.0,0.193:0.997,0.169:1.0,0.22:36;1456,95;88 chrMT 316 . G C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1841:0.009:0.005:0.014:16;0 chrMT 318 . T C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1784:0.003:0.001:0.008:6;0 chrMT 326 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1990:0.003:0.001:0.006:5;0 chrMT 333 . T C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:2068:0.004:0.002:0.008:8;0 chrMT 357 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:2271:0.002:0.001:0.005:5;0 chrMT 366 . G A . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:2251:0.002:0.001:0.005:5;0 chrMT 432 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1639:0.004:0.001:0.008:2;4 chrMT 435 . C A . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:2413:0.002:0.001:0.005:5;0 chrMT 439 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1617:0.015:0.01:0.022:23;1 chrMT 441 . C A . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:2221:0.002:0.001:0.005:5;0 chrMT 442 . T A,C . PASS AC=1,1;AN=3 GT:DP:HF:CILOW:CIUP:SDP 0/1/2:1671:0.003,0.004:0.001,0.002:0.007,0.009:5;0,7;0 chrMT 444 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1983:0.003:0.001:0.007:3;3 chrMT 446 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1850:0.003:0.001:0.007:6;0 chrMT 448 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1944:0.003:0.001:0.007:5;1 chrMT 451 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1888:0.003:0.001:0.006:3;2 chrMT 456 . C T . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:2242:0.002:0.001:0.005:5;0 chrMT 464 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1135:0.032:0.023:0.044:32;4 chrMT 466 . T C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1554:0.003:0.001:0.008:5;0 chrMT 470 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1895:0.015:0.01:0.021:28;0 chrMT 471 . T G . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1800:0.003:0.001:0.007:0;5 chrMT 478 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1894:0.003:0.001:0.006:5;0 chrMT 484 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:2063:0.004:0.002:0.008:8;0 chrMT 485 . T G . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:2020:0.002:0.001:0.006:0;5 chrMT 499 . G C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:2043:0.03:0.023:0.038:60;1 chrMT 503 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1724:0.012:0.008:0.019:21;0 chrMT 508 . A C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1640:0.004:0.002:0.009:6;1 chrMT 511 . CAG C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1953:0.012:0.008:0.018:15;9 chrMT 512 . AGC A,CGC . PASS AC=1,1;AN=3 GT:DP:HF:CILOW:CIUP:SDP 0/1/2:1856:0.008,0.005:0.004,0.002:0.013,0.009:5;9,9;0 chrMT 513 . GCA G,CCA . PASS AC=1,1;AN=2 GT:DP:HF:CILOW:CIUP:SDP None:2346:1.0,0.003:0.998,0.001:1.0,0.007:1154;1192,6;0 chrMT 515 . A G . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:175:0.114:0.075:0.171:8;12 chrMT 518 . CA C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:2095:0.004:0.002:0.008:6;3 chrMT 520 . CA C . PASS AC=1;AN=2 GT:DP:HF:CILOW:CIUP:SDP 0/1:1998:0.003:0.001:0.007:5;1