Question

Rename field annotated with SnpSift

0

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8.9 years ago

mavershang ▴ 60

Hi there.

I am using "snpSift annotate" to annotate a variant vcf file with two database file also in VCF format (say db1.vcf and db2.vcf).

Unfortunately, the fields I am interested in both db VCF files are named "AF", which cause confusion in the output. For example, see the end of this line

# Confusing part: AF=0.917931;AF=0.6812
# Full line below:
1    990517    rs2710872    C    T    1546.77    PASS   AC=2;AN=2;BaseQRankSum=1.660;ClippingRankSum=-0.289;DP=48;FS=3.802;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.217;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=32.22;ReadPosRankSum=-1.516;VQSLOD=-1.616e-01;culprit=FS;ANN=T|3_prime_UTR_variant|MODIFIER|AGRN|ENSG00000188157|transcript|ENST00000379370|protein_coding|36/36|c.*156C>T|||||156|,T|upstream_gene_variant|MODIFIER|RP11-465B22.3|ENSG00000217801|transcript|ENST00000427998|processed_transcript||n.-1C>T|||||4597|,T|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|transcript|ENST00000419249|protein_coding||c.*813C>T|||||1187|WARNING_TRANSCRIPT_INCOMPLETE,T|non_coding_exon_variant|MODIFIER|RP11-54O7.14|ENSG00000242590|transcript|ENST00000418300|sense_intronic|1/2|n.105C>T||||||,T|non_coding_exon_variant|MODIFIER|AGRN|ENSG00000188157|transcript|ENST00000461111|retained_intron|3/3|n.2410C>T||||||;RS=2710872;AF=0.917931;AF=0.6812

So I am just wondering if there is any way to define the field as a new name when doing SnpSift Annotate.

Thanks in advance.

SNP • 2.5k views

ADD COMMENT • link updated 15 months ago by Ram 43k • written 8.9 years ago by mavershang ▴ 60

0

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replace the original AF with 'sed' info before processing with SnpSift ?

ADD REPLY • link 8.9 years ago by Pierre Lindenbaum 161k

0

Entering edit mode

Good idea! I was carried away with snpSift.

The only negative side of this solution is that I need to do sed 4 times

ADD REPLY • link 8.9 years ago by mavershang ▴ 60

Ram · Answer 1 · 2015-05-22

I recently wrote a tool similar to "SnpSift annotate". It peeks info fields from a vcf-database indexed with tabix or tribble. https://github.com/lindenb/jvarkit/wiki/VcfPeekVcf

One option of this program is -p (prefix); = all the new INFO fields will be prefixed with this word.

$ java -jar dist/vcfpeekvcf.jar -f dbsnp_135.b37.vcf.gz -t GENEINFO,VP -p 00_NCBI135_  -i ExAC.r0.3.sites.vep.vcf.gz |\
grep NCBI135_ 


##INFO=<ID=00_NCBI135_GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id.  The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)">
##INFO=<ID=00_NCBI135_VP,Number=1,Type=String,Description="Variation Property">
##VcfPeekVcfCmdLine=-f /commun/data/pubdb/broadinstitute.org/bundle/1.5/b37/dbsnp_135.b37.vcf.gz -t GENEINFO,VP -p 00_NCBI135_ -i /commun/data/pubdb/broadinstitute.org/exac/0.3/ExAC.r0.3.sites.vep.vcf.gz
1   69428   rs140739101 T   G   4604953.42  PASS    00_NCBI135_GENEINFO=.;00_NCBI135_VP=050200000004040000000100;AC=2141;AC_AFR=20;AC_AMR=53;AC_Adj=1985;AC_EAS=0;AC_FIN=166;AC_Het=493;AC_Hom=746;AC_NFE=1668;AC_OTH=17;AC_SAS=61;AF=0.022;AN=99358;AN_AFR=7834;AN_AMR=6588;AN_Adj=80618;AN_EAS=8396;AN_FIN=3590;AN_NFE=41104;AN_OTH=626;AN_SAS=12480;BaseQRankSum=2.19;ClippingRankSum=-4.240e-01;DB;DP=1131603;FS=11.924;GQ_HIST=1523|6341|94|79|1292|32|35|13|11|10|20|12|24526|8836|2118|1909|782|234|274|1538,7|17|25|10|7|6|16|4|9|5|15|10|6|2|7|4|7|1|5|1190;GQ_MEAN=75.91;GQ_STDDEV=202.08;Het_AFR=10;Het_AMR=11;Het_EAS=0;Het_FIN=28;Het_NFE=418;Het_OTH=5;Het_SAS=21;Hom_AFR=5;Hom_AMR=21;Hom_EAS=0;Hom_FIN=69;Hom_NFE=625;Hom_OTH=6;Hom_SAS=20;InbreedingCoeff=0.3731;MQ=27.17;MQ0=0;MQRankSum=-1.014e+00;NCC=18661;QD=14.64;ReadPosRankSum=1.08;VQSLOD=44.51;culprit=MQ
1   69453   rs142004627 G   A   6724.79 VQSRTrancheSNP99.90to99.95  00_NCBI135_GENEINFO=.;00_NCBI135_VP=050200000004000000000100;AC=12;AC_AFR=3;AC_AMR=4;AC_Adj=7;AC_EAS=0;AC_FIN=0;AC_Het=1;AC_Hom=3;AC_NFE=0;AC_OTH=0;AC_SAS=0;AF=1.181e-04;AN=101644;AN_AFR=7954;AN_AMR=6638;AN_Adj=81032;AN_EAS=8402;AN_FIN=3606;AN_NFE=41318;AN_OTH=626;AN_SAS=12488;BaseQRankSum=0.742;ClippingRankSum=-6.150e-01;DB;DP=1001026;FS=90.555;GQ_HIST=1494|6818|211|263|1616|53|26|16|8|3|4|3|25002|9059|2178|1982|821|251|319|695,1|0|0|0|1|1|1|0|1|0|0|0|0|0|0|0|1|0|0|2;GQ_MEAN=53.93;GQ_STDDEV=24.34;Het_AFR=1;Het_AMR=0;Het_EAS=0;Het_FIN=0;Het_NFE=0;Het_OTH=0;Het_SAS=0;Hom_AFR=1;Hom_AMR=2;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_SAS=0;InbreedingCoeff=0.0192;MQ=28.57;MQ0=0;MQRankSum=1.54;NCC=17104;QD=22.95;ReadPosRankSum=-4.060e-01;VQSLOD=-4.645e+01;culprit=FS
1   69496   rs150690004 G   A   323905.92   VQSRTrancheSNP99.60to99.80  00_NCBI135_GENEINFO=.;00_NCBI135_VP=050200000004040000000100;AC=62;AC_AFR=46;AC_AMR=11;AC_Adj=59;AC_EAS=0;AC_FIN=0;AC_Het=35;AC_Hom=12;AC_NFE=2;AC_OTH=0;AC_SAS=0;AF=6.729e-04;AN=92132;AN_AFR=7748;AN_AMR=6566;AN_Adj=79928;AN_EAS=8388;AN_FIN=3570;AN_NFE=40582;AN_OTH=624;AN_SAS=12450;BaseQRankSum=2.12;ClippingRankSum=-1.529e+00;DB;DP=991114;FS=8.274;GQ_HIST=893|4697|202|135|905|245|364|326|147|307|231|164|22619|8691|2105|1925|794|250|316|750,0|0|0|0|1|0|0|0|0|1|1|0|0|0|0|1|0|0|0|46;GQ_MEAN=57.92;GQ_STDDEV=73.03;Het_AFR=24;Het_AMR=9;Het_EAS=0;Het_FIN=0;Het_NFE=2;Het_OTH=0;Het_SAS=0;Hom_AFR=11;Hom_AMR=1;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_SAS=0;InbreedingCoeff=0.0180;MQ=40.87;MQ0=0;MQRankSum=1.84;NCC=23714;NEGATIVE_TRAIN_SITE;QD=32.93;ReadPosRankSum=2.93;VQSLOD=-3.741e+00;culprit=MQ
1   69511   rs75062661  A   G   120729371.20    PASS    00_NCBI135_GENEINFO=OR4F5:79501;00_NCBI135_VP=050200000000000110000100;AC=75589;AC_AFR=4392;AC_AMR=6155;AC_Adj=72743;AC_EAS=8379;AC_FIN=3289;AC_Het=1789;AC_Hom=35477;AC_NFE=37731;AC_OTH=572;AC_SAS=12225;AF=0.894;AN=84570;AN_AFR=7392;AN_AMR=6474;AN_Adj=77432;AN_EAS=8384;AN_FIN=3320;AN_NFE=38832;AN_OTH=596;AN_SAS=12434;BaseQRankSum=0.831;ClippingRankSum=1.06;DB;DP=3157075;FS=23.500;GQ_HIST=1057|1461|500|275|204|94|127|139|117|163|175|204|1594|421|305|431|495|416|553|33554,71|556|484|263|161|89|124|138|114|159|175|198|273|346|295|424|491|416|553|33550;GQ_MEAN=224.54;GQ_STDDEV=255.92;Het_AFR=1030;Het_AMR=157;Het_EAS=5;Het_FIN=11;Het_NFE=461;Het_OTH=12;Het_SAS=113;Hom_AFR=1681;Hom_AMR=2999;Hom_EAS=4187;Hom_FIN=1639;Hom_NFE=18635;Hom_OTH=280;Hom_SAS=6056;InbreedingCoeff=0.6382;MQ=31.34;MQ0=0;MQRankSum=-4.020e-01;NCC=29303;QD=26.34;ReadPosRankSum=-1.106e+00;VQSLOD=131.28;culprit=FS
1   69534   rs190717287 T   C   109944.08   PASS    00_NCBI135_GENEINFO=.;00_NCBI135_VP=050200000000000010000100;AC=27;AC_AFR=0;AC_AMR=0;AC_Adj=26;AC_EAS=26;AC_FIN=0;AC_Het=20;AC_Hom=3;AC_NFE=0;AC_OTH=0;AC_SAS=0;AF=3.005e-04;AN=89844;AN_AFR=7810;AN_AMR=6532;AN_Adj=78908;AN_EAS=8392;AN_FIN=3344;AN_NFE=39788;AN_OTH=606;AN_SAS=12436;BaseQRankSum=5.94;ClippingRankSum=0.131;DB;DP=1383040;FS=0.000;GQ_HIST=424|4210|191|117|539|33|26|18|3|4|1|2|28777|7095|1331|1167|439|98|77|370,0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|23;GQ_MEAN=58.29;GQ_STDDEV=53.52;Het_AFR=0;Het_AMR=0;Het_EAS=20;Het_FIN=0;Het_NFE=0;Het_OTH=0;Het_SAS=0;Hom_AFR=0;Hom_AMR=0;Hom_EAS=3;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_SAS=0;InbreedingCoeff=0.0081;MQ=38.81;MQ0=0;MQRankSum=0.393;NCC=26044;QD=16.32;ReadPosRankSum=0.777;VQSLOD=-1.477e+00;culprit=MQ
1   69552   rs55874132  G   T,A,C   6289.25 VQSRTrancheSNP99.60to99.80  00_NCBI135_GENEINFO=OR4F5:79501;00_NCBI135_VP=050300000000040400000100;AC=3,3,5;AC_AFR=0,0,0;AC_AMR=3,0,0;AC_Adj=3,3,0;AC_EAS=0,0,0;AC_FIN=0,0,0;AC_Het=1,1,0,0,0,0;AC_Hom=1,1,0;AC_NFE=0,0,0;AC_OTH=0,0,0;AC_SAS=0,3,0;AF=3.308e-05,3.308e-05,5.514e-05;AN=90684;AN_AFR=7828;AN_AMR=6546;AN_Adj=79012;AN_EAS=8394;AN_FIN=3354;AN_NFE=39846;AN_OTH=606;AN_SAS=12438;BaseQRankSum=0.736;ClippingRankSum=0.198;DB;DP=1383162;FS=1.848;GQ_HIST=533|4275|91|84|874|13|15|4|2|0|1|0|28889|7105|1334|1168|438|98|75|343,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2,1|2|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_MEAN=57.16;GQ_STDDEV=20.29;Het_AFR=0,0,0,0,0,0;Het_AMR=1,0,0,0,0,0;Het_EAS=0,0,0,0,0,0;Het_FIN=0,0,0,0,0,0;Het_NFE=0,0,0,0,0,0;Het_OTH=0,0,0,0,0,0;Het_SAS=0,1,0,0,0,0;Hom_AFR=0,0,0;Hom_AMR=1,0,0;Hom_EAS=0,0,0;Hom_FIN=0,0,0;Hom_NFE=0,0,0;Hom_OTH=0,0,0;Hom_SAS=0,1,0;InbreedingCoeff=0.0345;MQ=30.21;MQ0=0;MQRankSum=-1.231e+00;NCC=25596;QD=9.65;ReadPosRankSum=0.920;VQSLOD=-2.686e+00;culprit=MQ
1   69590   rs141776804 T   A   222918.56   PASS    00_NCBI135_GENEINFO=.;00_NCBI135_VP=050200000004000000000100;AC=110;AC_AFR=1;AC_AMR=102;AC_Adj=103;AC_EAS=0;AC_FIN=0;AC_Het=37;AC_Hom=33;AC_NFE=0;AC_OTH=0;AC_SAS=0;AF=1.172e-03;AN=93836;AN_AFR=7862;AN_AMR=8636;AN_Adj=83862;AN_EAS=8438;AN_FIN=3596;AN_NFE=41696;AN_OTH=630;AN_SAS=13004;BaseQRankSum=0.266;ClippingRankSum=-8.820e-01;DB;DP=1437071;FS=0.000;GQ_HIST=150|4009|30|54|880|37|22|5|6|8|9|15|30709|7422|1387|1208|454|97|77|339,1|2|0|2|0|0|0|0|0|1|0|1|1|0|0|0|0|0|0|68;GQ_MEAN=58.94;GQ_STDDEV=53.31;Het_AFR=1;Het_AMR=36;Het_EAS=0;Het_FIN=0;Het_NFE=0;Het_OTH=0;Het_SAS=0;Hom_AFR=0;Hom_AMR=33;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_SAS=0;InbreedingCoeff=0.0538;MQ=39.62;MQ0=0;MQRankSum=0.559;NCC=23145;QD=18.54;ReadPosRankSum=0.033;VQSLOD=-2.401e-01;culprit=MQ