Extracting Allele Frequencies at a set of given positions
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24 months ago
kmkdesilva ▴ 90

Hi all,

I used SIFT annotator on a vcf file containing 96 animals. After annotation there is a new "SIFTINFO=" tag in the info field of the vcf file which gives the information on whether the variant is tolerated, deleterious or NA. I would like to extract the Allele Frequency(AF) at these positions. I appreciate if someone can give me an insight on how to do this.

Allele Frequnecy VCF Whole genome DNA sequence • 431 views
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Hello kmkdesilva,

could you please show some example lines of your vcf and the expected output?

Very likely bcftools query will help you with this task.

fin swimmer

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chr1    183     .       GA      G       547.21  .       AC=6;AF=0.750;AN=8;DP=77;ExcessHet=0.3218;FS=0.000;MLEAC=54;MLEAF=1.00;MQ=47.12;MQ0=0;QD=28.73;SOR=0.693        GT:AD:DP:GQ:PL  ./.:0,0:0:.:0,0,0       0/0:8,0:8:3:0,3,45      ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0./.:2,0:2:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:2,0:2:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:1,0:1:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:2,0:2:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0./.:0,0:0:.:0,0,0       ./.:1,0:1:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:6,0:6:.:0,0,0       ./.:0,0:
chr1    19845   .       T       C       991.94  .       AC=25;AF=0.305;AN=82;BaseQRankSum=-7.310e-01;ClippingRankSum=0.731;DP=181;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.4858;MLEAC=51;MLEAF=0.622;MQ=5.58;MQ0=0;MQRankSum=-7.310e-01;QD=33.06;RAW_MQ=1682.00;ReadPosRankSum=-7.310e-01;SOR=0.693;SIFTINFO=C|ENSBTAT00000064346|ENSBTAG00000046619|5S_rRNA|rRNA|NONCODING|NA/NA|NA|NA|NA|NA|rs478974503|NA GT:AD:DP:GQ:PL  1/1:0,2:2:6:68,6,0      1/1:0,2:2:6:70,6,0      ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       0/0:7,0:7:2:0,2,222     1/1:0,1:1:3:27,3,0./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       0/0:2,0:2:6:0,6,54      ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:1,0:1:.:0,0,0       1/1:0,3:3:9:83,9,0      0/0:7,0:7:0:0,0,194     0/1:1,4:5:28:77,0,28    ./.:0,0:0:.:0,0,0       0/0:1,0:1:0:0,0,27      0/0:3,0:3:9:0,9,98      0/0:2,0:2:6:0,6,53      0/0:2,0:2:6:0,6,71      0/0:5,0:5:9:0,9,135     ./.:1,0:1:.:0,0,0       0/0:6,0:6:0:0,0,79      0/0:3,0:3:6:0,6,71      0/0:9,0:9:0:0,0,272./.:2,0:2:.:0,0,0       ./.:0,0:0:.:0,0,0       1/1:0,3:3:9:90,9,0      ./.:0,0:0:.:0,0,0       ./.:1,0:1:.:0,0,0       ./.:0,0:0:.:0,0,0       ./.:2,0:2:.:0,0,0       ./.:0,0:0:.:0,0,0       0/0:3,0:3:9:0,9,78      ./.:0,0:0:.:0,0,0       1/1:0,2:2:6:68,6,0      ./.:0,0:0:.:0,0,0       ./.:0,0:0:.:0,0,
chr1    70226   .       C       T,A     6330.98 .       AC=72,11;AF=0.375,0.057;AN=192;BaseQRankSum=-2.710e-01;ClippingRankSum=0.00;DP=840;ExcessHet=0.3050;FS=294.381;InbreedingCoeff=0.1125;MLEAC=72,12;MLEAF=0.375,0.063;MQ=4.55;MQ0=0;MQRankSum=0.358;QD=13.64;RAW_MQ=9614.00;ReadPosRankSum=0.358;SOR=9.781;SIFTINFO=A|ENSBTAT00000052762|ENSBTAG00000039257|NA|CDS|NONSYNONYMOUS|R/L|298|1.000|2.68|299|novel|TOLERATED,T|ENSBTAT00000052762|ENSBTAG00000039257|NA|CDS|NONSYNONYMOUS|R/H|298|0.046|2.68|299|rs207604905|DELETERIOUS       GT:AD:DP:GQ:PL  0/0:10,0,0:10:0:0,0,138,0,138,138       0/2:6,0,4:10:96:96,114,313,0,199,187    0/0:16,0,0:16:33:0,33,576,33,576,576    0/0:10,0,0:10:22:0,22,319,22,319,319    0/1:8,5,0:13:99:142,0,179,166,194,360   1/1:0,3,0:3:9:101,9,0,101,9,101 0/0:5,0,0:5:0:0,0,32,0,32,32    1/1:0,5,0:5:15:183,15,0,183,15,183      0/1:3,2,0:5:53:53,0,54,62,60,122        1/1:0,2,0:2:6:68,6,0,68,6,68    0/1:6,3,0:9:74:74,0,189,92,198,290      1/1:0,2,0:2:6:75,6,0,75,6,75    0/1:7,2,0:9:45:45,0,213,67,219,286      0/2:6,0,5:11:99:122,140,316,0,177,161   0/0:9,0,0:9:26:0,26,315,26,315,315      0/1:5,4,0:9:85:85,0,121,99,133,232      0/1:7,4,0:11:99:109,0,187,130,199,329   0/0:5,0,0:5:9:0,9,135,9,135,135 0/1:8,3,0:11:75:75,0,230,99,239,338     0/0:16,0,0:16:39:0,39,585,39,585,585    0/1:9,3,0:12:70:70,0,223,97,232,329     0/0:7,0,0:7:21:0,21,260,

Three lines are given above. The positions annotated by SIFT software has the "SIFTINFO=" tag in the info field. I want to extract the AF of the SIFT annotated DELETERIOUS positions.

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