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Extracting Allele Frequencies at a set of given positions

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
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written by Kash Kash

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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written by finswimmer finswimmer 
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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updated by finswimmer finswimmer • written by Kash Kash

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