Problems While Filtering Rare Variants With Annovar

Question

[farah]

Hello, I am trying to filter out common variants to get my rare varianst using Annovar. I got everything as invalid input! I got nothing in my filtered file, everything was in the invalid input I used the command: annotate_variation.pl -filter -dbtype 1000g2012apr_eur -buildver hg19 myfile.vcf humandb/ -maf 0.1

NOTICE: Variants matching filtering criteria are written to myfile.vcf.hg19_EUR.sites.2012_04_dropped, other variants are written to myfile.vcf.hg19_EUR.sites.2012_04_filtered NOTICE: Processing next batch with 0 unique variants in 232105 input lines NOTICE: Database index loaded. Total number of bins is 2766067 and the number of bins to be scanned is 0 NOTICE: Scanning filter database /humandb/hg19_EUR.sites.2012_04.txt...Done NOTICE: Variants with invalid input format were written to myfile.vcf.invalid_input

Can someone help? Thank you very much

[Jorge Amigo]

that seems like a format problem. showing a little bit of the input file here would definitely help.

[farah]

here is some of my input:

1       16780   .       G       A       401.18  VQSRTrancheBOTH99.00to99.90     AC=2;AF=1.672e-03;AN=1196;BaseQRankSum=-5.323;DP=25463;Dels=0.00;FS=0.000;HaplotypeScore=0.6584;InbreedingCoeff=-0.0351;MLEAC=1;MLEAF=8.361e-04;MQ=38.31;MQ0=0;MQRankSum=0.291;QD=4.51;ReadPosRankSum=-2.640;VQSLOD=-3.540e+00;culprit=MQ       GT:AD:DP:GQ:PL  ./.     ./.     ./.     ./.     ./.     0/0:18,0:18:54:0,54,602 0/0:14,0:14:42:0,42,446 0/0:8,0:8:24:0,24,267   0/0:13,0:13:27:0,27,333 0/0:20,0:20:51:0,51,538 0/0:23,0:23:54:0,54,607 0/0:15,0:15:39:0,39,415 0/0:33,0:33:96:0,96,1006        0/0:27,0:27:69:0,69,710 0/0:15,0:15:42:0,42,415 0/0:22,0:22:60:0,60,673 0/0:20,0:20:60:0,60,669 0/0:61,0:61:99:0,183,1863       0/0:93,0:93:99:0,280,2845       0/0:66,0:66:99:0,198,2019       0/0:101,0:101:99:0,304,3090     ./.     ./.     0/0:2,0:2:6:0,6,55
      ./.     ./.     ./.     ./.     ./.     ./.     ./.     0/0:1,0:1:3:0,3,28      ./.     0/0:157,0:157:99:0,445,4553     0/0:129,0:129:99:0,388,4062     0/0:165,0:165:99:0,493,5269     0/0:158,0:158:99:0,472,4922     0/0:180,0:180:99:0,526,5292     0/0:139,0:139:99:0,415,4344     0/0:128,0:128:99:0,385,4157     0/0:179,0:179:99:0,526,5465     0/0:204,0:204:99:0,583,5885     0/0:188,0:188:99:0,544,5615     0/0:153,0:153:99:0,457,4746     0/0:144,0:144:99:0,433,4519     0/0:150,0:150:99:0,451,4588     0/0:127,0:127:99:0,382,3885     0/0:127,0:127:99:0,382,4127     0/0:191,0:191:99:0,565,5694     0/0:164,0:164:99:0,490,4987     0/0:127,0:127:99:0,382,4007
     0/0:182,0:182:99:0,541,5621     0/0:129,0:129:99:0,388,4064     0/0:129,0:129:99:0,388,4062     0/0:130,0:130:99:0,391,4091     0/0:169,0:169:99:0,502,5074     0/0:190,0:190:99:0,556,5580     ./.     0/0:4,0:4:9:0,9,101     ./.     ./.     ./.     ./.     0/0:1,0:1:3:0,3,29      0/0:124,0:124:99:0,361,3854     0/0:130,0:130:99:0,370,3819     0/0:1,0:1:3:0,3,28      ./.     0/0:1,0:1:3:0,3,34      ./.     0/0:1,0:1:3:0,3,28      ./.     ./.     0/0:128,0:128:99:0,385,4270     ./.     0/0:2,0:2:6:0,6,63      ./.     0/0:1,0:1:3:0,3,28      0/0:27,0:27:72:0,72,742 ./.     0/0:68,0:68:99:0,205,2210       0/0:54,0:54:99:0,162,1801       0/0:57,0:57:99:0,168,1837       0/0:35,0:35:99:0,105,1170       0/0:40,0:40:99:0,120,1262       0/0:38,0:38:99:0,99,1082        0/0:57,0:57:99:0,168,1837       0/0:46,0:46:99:0,138,1495

[Matthieu Miossec]

Do you have any error output files? If so, post them please.

[farah]

the dropped and the filter files are both empty! I have only an invalid input file that it exactly like the input file. the errors i got i believe are the one summarized above as "NOTICE: Processing next batch with 0 unique variants in 232105 input lines NOTICE: Database index loaded. Total number of bins is 2766067 and the number of bins to be scanned is 0"

Answer 1

[DG]

Looks like you are feeding annovar filter a vcf file directly, which you can't do. One of the annoying things about annovar is you first need to convert your vcf file to an annovar format file, which is basically a tab delimited text file. See Annovar: Preparing Your Input File

[farah]

thanks a lot for drawing my attention to this

Answer 2

[Tky]

Another solution is to use wannovar, the online version of annovar which support VCF/GFF3 and annovar format (although the task takes longer time to run than a local installed annovar when your input file is big ) Hope this may helps, http://wannovar.usc.edu/

Answer 3

[amitkishore]

wANNOVAR is much user friendly with several filtering option and links the output to phenolyzer for visualization of gene interaction with particular phenotype (if this is also among one of your focus).