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edgardomortiz / vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
GNU General Public License v3.0
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Invalid character * in the alignment #35

Closed Rahmmy closed 3 years ago

Rahmmy commented 3 years ago

Hello, Thanks for this amazing script. I converted a 264 sample vcf file into a fasta alignment using vcf2phylip with default parameters. And attempted constructing a phylogeny using iqtree. this was unsuccessful because of the presence of invalid * characters in multiple sites in the alignment. Any recommendations?

edgardomortiz commented 3 years ago

If you email me a few thousand lines from your VCF I might be able to diagnose the issue.

Edgardo

giyany commented 3 years ago

Hi, I encountered the same issue with our fasta alignment. Was there any insight on the issue?

linsson commented 3 years ago

Same problem, iqtree doesn't like "*"

I cannot send a vcf file but this is an extract of it:

CHROM POS REF ALT 011080 011660 134660 134670

SL4.0ch01 81479 C T 1/1:1,47:48:99:.:.:1286,116,0:. 1/1:0,10:10:30:.:.:291,30,0:. 1/1:0,50:50:99:.:.:1488,150,0:. 1/1:3,38:41:34:.:.:1070,34,0:. SL4.0ch01 117424 A G 1|1:2,37:39:55:1|1:117420_T_C:808,55,0:117420 1/1:0,15:15:44:.:.:315,44,0:. 1/1:4,47:51:19:.:.:986,19,0:. 1/1:2,46:48:86:.:.:1051,86,0:. SL4.0ch01 139548 C T,A 1/1:0,55,0:55:99:.:.:1633,165,0,1633,165,1633:. 0/1:3,15,0:18:25:.:.:356,0,25,365,69,434:. 0/0:48,0,0:48:99:.:.:0,100,1407,100,1407,1407:. 0/0:48,0,0:48:99:.:.:0,109,1252,109,1252,1252:. SL4.0ch01 179250 G T,,C 1/1:1,49,0,0:50:99:.:.:1524,120,0,1527,147,1555,1527,147,1555,1555:. 1/1:0,12,0,0:12:36:.:.:357,36,0,357,36,357,357,36,357,357:. 1/1:1,49,0,0:50:99:.:.:1521,115,0,1524,146,1554,1524,146,1554,1554:. 1/1:1,51,0,0:52:99:.:.:1588,121,0,1523,151,1511,1523,151,1511,1511:. SL4.0ch01 225060 A G 0/0:50,0:50:99:.:.:0,120,1800:. 0/0:10,0:10:30:.:.:0,30,246:. 0/0:50,0:50:99:.:.:0,104,1487:. 0/0:50,0:50:99:.:.:0,117,1374:. SL4.0ch01 290172 G A 0/0:35,0:35:74:.:.:0,74,870:. ./.:1,0:1:.:.:.:0,0,0:. 1/1:1,39:40:91:.:.:1262,91,0:. 1/1:0,32:32:96:.:.:1121,96,0:. SL4.0ch01 323011 A T, 2/2:0,0,25:25:75:.:.:939,939,939,75,75,0:. 2/2:0,0,2:2:6:.:.:76,76,76,6,6,0:. 2/2:1,0,28:32:56:.:.:1081,988,972,56,92,0:. 2/2:1,0,48:49:99:.:.:1786,1789,1825,108,144,0:.

Here are 4 accessions with at position 7; ALT is T, and their GT is 2/2. I just had a quick view in the code...I am not sure, really, I guess this part

nt_dict = {str(0): record[3].replace("-","").upper(), ".": "N"} # must be replaced by the REF in the ALT field for GVCFs from GATK alt = record[4].replace("-", "").replace("", `nt_dict["0"])

might have some relevance.

edgardomortiz commented 3 years ago

Hi @linsson ,

I requested some sample data from the original poster but got no reply. Could you send me a few thousand lines from the VCF to investigate the issue?

Edgardo

giyany commented 3 years ago

Hi,

Seeing that this discussion is ongoing, in the meantime I found the vcf contains a few indels, that I assumed were removed. Filtering them solved the issue as one would expect.

edgardomortiz commented 3 years ago

Great, good to know, would you mind pasting a couple of examples so I can parse them or skip them directly from the script?

giyany commented 3 years ago

Happily: you mean from the vcf file?

Scaffold_1028 95604 . G A, 7611.28 PASS AC=49,2;AF=0.583,0.024;AN=84;BaseQRankSum=0;DP=407;ExcessHet=0;FS=0;InbreedingCoeff=0.6958;MLEAC=71,2;MLEAF=0.657,0.019;MQ=38.86;MQRankSum=1;QD=34.13;ReadPosRankSum=1;SOR=0.6 07 GT:AD:DP:FT:GQ:PGT:PID:PL:PS 1/1:0,4,1:5:PASS:12:.:.:133,12,0,133,12,133:. 1/1:0,4,2:6:PASS:12:.:.:125,12,0,125,12,125:. ./.:2,0,0:2:genotypedepth:6:.:.:0,6,73,6,73,73:. 0/0:8,0,0:8:PASS:21:.:.:0,21,315,21,315,315: . ./.:2,0,0:2:genotypedepth:6:.:.:0,6,72,6,72,72:. ./.:0,0,0:0:PASS:.:.:.:0,0,0,0,0,0:. 2|2:0,0,6:6:PASS:19:1|1:95542_G_C:272,272,272,19,19,0:95542 ./.:7,0,0:7:PASS:.:.:.:0,0,0,0,0,0:. 0/0:10,0,0:10:PASS:0:.:.:0,0,107,0 ,107,107:. ./.:0,2,0:2:genotypedepth:6:.:.:49,6,0,49,6,49:. ./.:0,3,0:3:genotypedepth:9:.:.:113,9,0,113,9,113:. ./.:2,0,0:2:genotypedepth:6:.:.:0,6,72,6,72,72:. ./.:0,0,0:0:PASS:.:.:.:0,0,0,0,0,0:. ./.:1,0,0:1:PASS :.:.:.:0,0,0,0,0,0:. 1/1:0,6,0:6:PASS:18:.:.:235,18,0,235,18,235:. 1/1:0,5,0:5:PASS:15:.:.:171,15,0,171,15,171:. 1/1:0,9,0:9:PASS:27:.:.:376,27,0,376,27,376:. ./.:1,0,0:1:PASS:.:.:.:0,0,0,0,0,0:. ./.:0,0,0:0:PASS:.:.:.:0,0,0,0 ,0,0:. ./.:1,0,0:1:genotypedepth:3:.:.:0,3,42,3,42,42:. ./.:0,0,0:0:PASS:.:.:.:0,0,0,0,0,0:. 0/0:15,0,0:15:PASS:42:.:.:0,42,630,42,630,630:. 1/1:0,11,0:11:PASS:33:.:.:437,33,0,437,33,437:. 0/0:11,0,0:11:PASS:33:.:.:0,33,459,3 3,459,459:. 0/0:16,0,0:16:PASS:45:.:.:0,45,675,45,675,675:. 1/1:0,9,0:9:PASS:27:.:.:365,27,0,365,27,365:. 1/1:0,4,0:4:PASS:12:.:.:133,12,0,133,12,133:. 0/0:12,0,0:12:PASS:33:.:.:0,33,495,33,495,495:. 1/1:0,9,0:9:PASS:27:.:.:315,27,0,3 15,27,315:. ./.:0,3,0:3:genotypedepth:9:.:.:125,9,0,125,9,125:. 0/0:4,0,0:4:PASS:12:.:.:0,12,141,12,141,141:. ./.:2,0,0:2:genotypedepth:6:.:.:0,6,72,6,72,72:. 0/0:9,0,0:9:PASS:24:.:.:0,24,360,24,360,360:. 0/0:8,0,0:8:PASS :24:.:.:0,24,232,24,232,232:. 0/0:8,0,0:8:PASS:21:.:.:0,21,315,21,315,315:. 0/0:4,0,0:4:PASS:12:.:.:0,12,121,12,121,121:. ./.:2,0,0:2:PASS:.:.:.:0,0,0,0,0,0:. 1|1:0,9,0:9:PASS:27:1|1:95603_C_G:405,27,0,405,27,405:95603 1|1:0, 10,1:11:PASS:30:1|1:95603_C_G:450,30,0,450,30,450:95603 1/1:0,7,0:7:PASS:21:.:.:220,21,0,220,21,220:. 1/1:0,6,1:7:PASS:18:.:.:217,18,0,217,18,217:. ./.:0,0,0:0:PASS:.:.:.:0,0,0,0,0,0:. 1/1:0,13,0:13:PASS:39:.:.:539,39,0,539,39,53 9:. 1/1:0,4,0:4:PASS:12:.:.:158,12,0,158,12,158:. 1/1:0,9,0:9:PASS:26:.:.:295,26,0,295,26,295:. 1/1:0,11,0:11:PASS:33:.:.:394,33,0,394,33,394:. 1/1:0,4,2:6:PASS:12:.:.:154,12,0,154,12,154:. 1/1:0,10,0:10:PASS:30:.:.:427,30,0,427,30, 427:. 1|1:0,6,0:6:PASS:18:1|1:95603_C_G:270,18,0,270,18,270:95603 ./.:2,0,0:2:PASS:.:.:.:0,0,0,0,0,0:. ./.:2,0,0:2:PASS:.:.:.:0,0,0,0,0,0:. 0/0:11,0,0:11:PASS:33:.:.:0,33,413,33,413,413:. ./.:2,0,0:2:genotypedepth:6:.:.:0,6,84,6 ,84,84:. 0/0:8,0,0:8:PASS:24:.:.:0,24,322,24,322,322:. 0/0:16,0,0:16:PASS:48:.:.:0,48,600,48,600,600:. ./.:1,0,0:1:PASS:.:.:.:0,0,0,0,0,0:. 1/1:0,9,0:9:PASS:27:.:.:318,27,0,318,27,318:. 1/1:0,5,0:5:PASS:15:.:.:197,15,0,197,1 5,197:. 0/0:4,0,0:4:PASS:12:.:.:0,12,157,12,157,157:. 0/1:5,3,0:8:PASS:99:.:.:102,0,181,117,190,307:. 0/1:6,6,0:12:PASS:99:.:.:202,0,195,221,213,434:. ./.:0,0,0:0:PASS:.:.:.:0,0,0,0,0,0:. ./.:2,0,0:2:genotypedepth:6:.:.:0,6, 84,6,84,84:. 1/1:0,14,0:14:PASS:42:.:.:517,42,0,517,42,517:. 0/1:2,2,0:4:PASS:54:.:.:54,0,78,60,84,144:. ./.:2,0,0:2:genotypedepth:6:.:.:0,6,57,6,57,57:. ./.:1,0,0:1:genotypedepth:3:.:.:0,3,42,3,42,42:. Scaffold_1028 151063 . T . . PASS AN=82;DP=346 GT:DP:FT:RGQ ./.:0:PASS:0 ./.:1:genotypedepth:3 0/0:4:PASS:9 0/0:8:PASS:18 0/0:4:PASS:12 ./.:3:genotypedepth:9 ./.:2:genotypedepth:6 0/0:5: PASS:15 0/0:8:PASS:24 ./.:0:PASS:0 ./.:3:genotypedepth:9 0/0:4:PASS:12 ./.:1:genotypedepth:3 0/0:8:PASS:24 ./.:3:genotypedepth:9 ./.:3:genotypedepth:9 0/0:4:PASS:12 0/0:4:PASS:12 0/0:8:PASS:24 0/0:5:PASS:15 ./.: 1:genotypedepth:3 0/0:6:PASS:18 0/0:12:PASS:30 ./.:12:PASS:0 0/0:10:PASS:30 0/0:11:PASS:33 ./.:2:genotypedepth:6 0/0:9:PASS:24 0/0:11:PASS:33 ./.:2:genotypedepth:6 ./.:0:PASS:0 ./.:1:genotypedepth:3 ./.:3:genotypedept h:9 0/0:10:PASS:30 ./.:3:genotypedepth:9 ./.:3:genotypedepth:9 ./.:2:genotypedepth:6 0/0:5:PASS:15 0/0:11:PASS:33 0/0:8:PASS:24 0/0:8:PASS:24 0/0:5:PASS:15 0/0:9:PASS:27 0/0:9:PASS:21 0/0:11:PASS:30 0/0:15:PASS:42 ./.:3:genotypedepth:6 0/0:4:PASS:12 0/0:11:PASS:33 ./.:0:PASS:0 ./.:1:genotypedepth:3 0/0:4:PASS:12 0/0:4:PASS:12 0/0:4:PASS:9 ./.:2:genotypedepth:6 0/0:7:PASS:21 ./.:1:genotypedepth:3 ./.:1:genotypedepth:3 0/0:4: PASS:12 0/0:5:PASS:15 0/0:5:PASS:12 0/0:6:PASS:15 0/0:6:PASS:18 0/0:5:PASS:12 0/0:5:PASS:15 0/0:8:PASS:24 ./.:3:genotypedepth:9 Scaffold_1028 151067 . A . . PASS AN=82;DP=356 GT:DP:FT:RGQ ./.:0:PASS:0 ./.:1:genotypedepth:3 ./.:6:PASS:0 0/0:8:PASS:18 0/0:4:PASS:12 ./.:3:genotypedepth:9 ./.:2:genotypedepth:6 0/0:5: PASS:12 0/0:11:PASS:30 ./.:0:PASS:0 ./.:3:genotypedepth:9 0/0:4:PASS:9 ./.:1:genotypedepth:3 0/0:8:PASS:24 ./.:3:genotypedepth:6 ./.:3:genotypedepth:9 0/0:4:PASS:12 0/0:4:PASS:12 0/0:8:PASS:24 0/0:5:PASS:15 ./.: 1:genotypedepth:3 0/0:6:PASS:18 0/0:10:PASS:27 0/0:13:PASS:36 0/0:10:PASS:30 0/0:12:PASS:33 ./.:2:genotypedepth:6 0/0:9:PASS:24 0/0:12:PASS:36 ./.:2:genotypedepth:6 ./.:0:PASS:0 ./.:1:genotypedepth:3 ./.:3:genotypedept h:9 0/0:11:PASS:33 ./.:3:genotypedepth:9 ./.:3:genotypedepth:9 ./.:2:genotypedepth:6 0/0:6:PASS:18 0/0:11:PASS:33 0/0:8:PASS:24 0/0:8:PASS:24 0/0:5:PASS:15 0/0:9:PASS:24 0/0:7:PASS:18 0/0:11:PASS:30 0/0:14:PASS:42 ./.:2:genotypedepth:6 0/0:4:PASS:12 0/0:11:PASS:33 ./.:0:PASS:0 ./.:2:genotypedepth:6 0/0:4:PASS:12 0/0:5:PASS:15 0/0:5:PASS:12 ./.:2:genotypedepth:6 0/0:7:PASS:21 ./.:1:genotypedepth:3 ./.:1:genotypedepth:3 0/0:5: PASS:15 0/0:5:PASS:15 0/0:5:PASS:12 0/0:6:PASS:15 0/0:6:PASS:18 0/0:6:PASS:15 0/0:5:PASS:15 0/0:9:PASS:27 ./.:3:genotypedepth:9 Scaffold_1028 151068 . A . . PASS AN=82;DP=360 GT:DP:FT:RGQ ./.:0:PASS:0 ./.:1:genotypedepth:3 ./.:6:PASS:0 0/0:8:PASS:18 0/0:4:PASS:12 ./.:3:genotypedepth:9 ./.:2:genotypedepth:6 0/0:5: PASS:12 0/0:11:PASS:30 ./.:0:PASS:0 ./.:3:genotypedepth:9 0/0:4:PASS:9 ./.:1:genotypedepth:3 0/0:8:PASS:24 0/0:4:PASS:9 ./.:3:genotypedepth:9 0/0:4:PASS:12 0/0:4:PASS:12 0/0:8:PASS:24 0/0:5:PASS:15 ./.:1:genoty pedepth:3 0/0:6:PASS:18 0/0:10:PASS:27 ./.:12:PASS:0 0/0:10:PASS:30 0/0:12:PASS:33 ./.:2:genotypedepth:6 0/0:9:PASS:27 0/0:12:PASS:36 ./.:2:genotypedepth:6 ./.:0:PASS:0 ./.:1:genotypedepth:3 ./.:3:genotypedepth:9 0/ 0:12:PASS:36 ./.:3:genotypedepth:9 ./.:3:genotypedepth:9 ./.:2:genotypedepth:6 0/0:6:PASS:18 0/0:11:PASS:33 0/0:8:PASS:24 0/0:8:PASS:24 0/0:5:PASS:15 0/0:9:PASS:24 0/0:7:PASS:18 0/0:11:PASS:30 0/0:14:PASS:39 ./.:2:ge notypedepth:6 0/0:5:PASS:15 0/0:12:PASS:36 ./.:0:PASS:0 ./.:2:genotypedepth:6 0/0:4:PASS:12 0/0:5:PASS:15 0/0:5:PASS:12 ./.:2:genotypedepth:6 0/0:7:PASS:21 ./.:1:genotypedepth:3 ./.:1:genotypedepth:3 0/0:5:PASS:15 0/0:5:PASS:15 0/0:5:PASS:12 0/0:6:PASS:15 0/0:7:PASS:21 0/0:6:PASS:15 0/0:5:PASS:15 0/0:9:PASS:27 ./.:3:genotypedepth:9 Scaffold_1028 155472 . T C, 3012.69 PASS AC=12,2;AF=0.125,0.021;AN=96;BaseQRankSum=0;DP=556;ExcessHet=0;FS=1.485;InbreedingCoeff=0.5912;MLEAC=13,3;MLEAF=0.103,0.024;MQ=31.67;MQRankSum=0;QD=30.76;ReadPosRankSum=1;SOR =1.053 GT:AD:DP:FT:GQ:PGT:PID:PL:PS ./.:1,0,0:1:genotypedepth:3:.:.:0,3,30,3,30,30:. ./.:3,0,0:3:genotypedepth:9:.:.:0,9,125,9,125,125:. 1|1:0,24,0:24:PASS:72:1|1:155402_CAT_C:1080,72,0,1080,72,1080:155402 0/0:10,0,0:1 0:PASS:24:.:.:0,24,360,24,360,360:. 0/0:4,0,0:4:PASS:12:.:.:0,12,129,12,129,129:. ./.:2,0,0:2:genotypedepth:6:.:.:0,6,84,6,84,84:. ./.:3,0,0:3:genotypedepth:6:.:.:0,6,90,6,90,90:. 0/0:15,0,0:15:PASS:42:.:.:0,42,630,42,630, 630:. 0/0:18,0,0:18:PASS:48:.:.:0,48,720,48,720,720:. 0/0:7,0,0:7:PASS:0:.:.:0,0,209,0,209,209:. 0/0:5,0,0:5:PASS:0:.:.:0,0,42,0,42,42:. 1|1:0,9,0:9:PASS:27:1|1:155402_CAT_C:405,27,0,405,27,405:155402 ./.:0,0,0:0:PASS:.:.:.:0,0,0,0,0 ,0:. 1|1:0,24,0:24:PASS:72:1|1:155402_CAT_C:1080,72,0,1080,72,1080:155402 ./.:1,0,0:1:genotypedepth:3:.:.:0,3,42,3,42,42:. 0/0:6,0,0:6:PASS:18:.:.:0,18,213,18,213,213:. ./.:2,0,0:2:genotypedepth:6:.:.:0,6,62,6,62,62:. 0|1:3,2,1:6:PASS:75:0|1:155415_T_G:75,0,120,84,126,210:155415 0|1:6,3,0:9:PASS:99:0|1:155415_T_A:108,0,243,126,252,378:155415 0/0:4,0,0:4:PASS:12:.:.:0,12,124,12,124,124:. 1|1:0,4,0:4:PASS:12:1|1:155415_T_A:180,12,0,180,12,180 :155415 0/0:13,0,0:13:PASS:36:.:.:0,36,540,36,540,540:. 0/0:18,0,0:18:PASS:54:.:.:0,54,752,54,752,752:. 0/0:15,0,0:15:PASS:36:.:.:0,36,540,36,540,540:. 0/0:13,0,0:13:PASS:36:.:.:0,36,540,36,540,540:. 0/0:27,0,0:27:PASS:39:.:.:0,39,1036, 39,1036,1036:. ./.:3,0,0:3:genotypedepth:9:.:.:0,9,121,9,121,121:. 0/0:21,0,0:21:PASS:54:.:.:0,54,810,54,810,810:. 0/0:12,0,0:12:PASS:36:.:.:0,36,425,36,425,425:. 0/0:5,0,0:5:PASS:15:.:.:0,15,209,15,209,209:. ./.:1,0,0:1:genoty pedepth:3:.:.:0,3,42,3,42,42:. ./.:3,0,0:3:genotypedepth:9:.:.:0,9,113,9,113,113:. 0/0:4,0,0:4:PASS:12:.:.:0,12,141,12,141,141:. 0/0:17,0,0:17:PASS:45:.:.:0,45,675,45,675,675:. 2|2:0,0,4:4:PASS:12:1|1:155311_C_T:180,180,180,1 2,12,0:155311 ./.:0,0,1:1:genotypedepth:3:.:.:45,45,45,3,3,0:. ./.:3,0,0:3:genotypedepth:9:.:.:0,9,125,9,125,125:. 0/0:10,0,0:10:PASS:27:.:.:0,27,405,27,405,405:. 0/0:10,0,0:10:PASS:30:.:.:0,30,340,30,340,340:. 0/0:10,0,0:10: PASS:30:.:.:0,30,323,30,323,323:. ./.:1,0,0:1:genotypedepth:3:.:.:0,3,25,3,25,25:. 1|1:0,4,0:4:PASS:12:1|1:155402_CAT_C:180,12,0,180,12,180:155402 0/0:18,0,0:18:PASS:51:.:.:0,51,765,51,765,765:. 0/0:11,0,0:11:PASS:33:.:.:0,33,418,3 3,418,418:. 0/0:11,0,0:11:PASS:30:.:.:0,30,450,30,450,450:. 0/0:7,0,0:7:PASS:21:.:.:0,21,262,21,262,262:. 0/0:4,0,0:4:PASS:12:.:.:0,12,140,12,140,140:. 0/0:9,0,0:9:PASS:0:.:.:0,0,209,0,209,209:. 0/0:10,0,0:10:PASS:30:.:.:0,30,414 ,30,414,414:. 0/0:5,0,0:5:PASS:15:.:.:0,15,163,15,163,163:. 0/0:4,0,0:4:PASS:12:.:.:0,12,129,12,129,129:. ./.:3,0,0:3:genotypedepth:9:.:.:0,9,113,9,113,113:. 0/0:11,0,0:11:PASS:33:.:.:0,33,387,33,387,387:. 0/0:7,0,0:7:PASS:21:.:.: 0,21,280,21,280,280:. 0/0:15,0,0:15:PASS:42:.:.:0,42,630,42,630,630:. 0/0:10,0,0:10:PASS:30:.:.:0,30,387,30,387,387:. ./.:0,0,0:0:PASS:.:.:.:0,0,0,0,0,0:. ./.:1,0,0:1:genotypedepth:3:.:.:0,3,15,3,15,15:. ./.:3,0,0:3:genotypede pth:6:.:.:0,6,90,6,90,90:. 0/0:11,0,0:11:PASS:33:.:.:0,33,413,33,413,413:. 0/0:5,0,0:5:PASS:15:.:.:0,15,197,15,197,197:. 0/0:6,0,0:6:PASS:18:.:.:0,18,224,18,224,224:. ./.:9,0,0:9:PASS:.:.:.:0,0,0,0,0,0:. 0/0:12,0,0:12:PASS:3 6:.:.:0,36,489,36,489,489:. ./.:0,0,0:0:PASS:.:.:.:0,0,0,0,0,0:. 0/0:26,0,0:26:PASS:72:.:.:0,72,1080,72,1080,1080:. 0/0:6,0,0:6:PASS:18:.:.:0,18,239,18,239,239:. Scaffold_1028 155480 . C . . 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edgardomortiz commented 3 years ago

Great, thanks! I will try to fix it this afternoon

giyany commented 3 years ago

Thank you for your work! I use this tool all the time, it's simple and very fast.

edgardomortiz commented 3 years ago

@Rahmmy @linsson @giyany the Issue is solved, please re-clone the repository (v2.8) and try again, * represent deletions and they should show in the matrix as -. I had introduced the bug in v2.7, when I re-wrote most of the code.

Edgardo