Question: Freebayes on Galaxy shows vcf output with GT INFO field as 0/0
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gravatar for deepti1rao
4 months ago by
deepti1rao10
deepti1rao10 wrote:

Freebayes on Galaxy shows vcf output with GT INFO field as 0/0.

Chr1    10000171    .   G   A   6.18434e-10 .   AB=0;ABP=0;AC=0;AF=0;AN=2;AO=19;CIGAR=1X;DP=75;DPB=75;DPRA=0;EPP=5.8675;EPPR=3.16541;GTI=0;LEN=1;MEANALT=1;MQM=5.36842;MQMR=4.46429;NS=1;NUMALT=1;ODDS=22.6724;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=733;QR=2219;RO=56;RPL=9;RPP=3.12459;RPPR=33.4109;RPR=10;RUN=1;SAF=8;SAP=4.03889;SAR=11;SRF=27;SRP=3.16541;SRR=29;TYPE=snp  GT:DP:AD:RO:QR:AO:QA:GL 0/0:75:56,19:56:2219:19:733:0,-13.3474,-13.3067
Chr1    10000229    .   G   A   0   .   AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=6.20364;EPPR=8.05372;GTI=0;LEN=1;MEANALT=1;MQM=5.05882;MQMR=5.20968;NS=1;NUMALT=1;ODDS=48.306;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=675;QR=2512;RO=62;RPL=11;RPP=6.20364;RPPR=5.25182;RPR=6;RUN=1;SAF=5;SAP=9.26925;SAR=12;SRF=30;SRP=3.15039;SRR=32;TYPE=snp  GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:62,17:62:2512:17:675:0,-15.9933,-21.3255
Chr1    10000289    .   C   T   7.85182e-12 .   AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.55317;EPPR=10.4997;GTI=0;LEN=1;MEANALT=1;MQM=5.5;MQMR=4.71429;NS=1;NUMALT=1;ODDS=27.0391;PAIRED=1;PAIREDR=0.979592;PAO=0;PQA=0;PQR=0;PRO=0;QA=600;QR=1909;RO=49;RPL=10;RPP=5.18177;RPPR=4.11819;RPR=6;RUN=1;SAF=5;SAP=7.89611;SAR=11;SRF=21;SRP=5.18177;SRR=28;TYPE=snp  GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:49,16:49:1909:16:600:0,-11.602,-12.7964
Chr1    10000347    .   C   T   1.46408e-07 .   AB=0;ABP=0;AC=0;AF=0;AN=2;AO=11;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=4.78696;EPPR=4.27278;GTI=0;LEN=1;MEANALT=1;MQM=5.18182;MQMR=3.67442;NS=1;NUMALT=1;ODDS=17.2054;PAIRED=1;PAIREDR=0.976744;PAO=0;PQA=0;PQR=0;PRO=0;QA=414;QR=1669;RO=43;RPL=3;RPP=7.94546;RPPR=5.48477;RPR=8;RUN=1;SAF=3;SAP=7.94546;SAR=8;SRF=13;SRP=17.6046;SRR=30;TYPE=snp    GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:43,11:43:1669:11:414:0,-11.0844,-9.07387
Chr1    10000467    .   G   A   7.44984 .   AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.73412;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=3.33333;MQMR=2.85714;NS=1;NUMALT=1;ODDS=1.51707;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=278;RO=7;RPL=2;RPP=3.73412;RPPR=10.7656;RPR=1;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=1;SRP=10.7656;SRR=6;TYPE=snp    GT:DP:AD:RO:QR:AO:QA:GL 0/0:10:7,3:7:278:3:110:0,-2.07745,-0.895333
Chr1    10000524    .   C   A   0.296537    .   AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=4.45795;EPPR=3.49285;GTI=0;LEN=1;MEANALT=1;MQM=4.16667;MQMR=3.94444;NS=1;NUMALT=1;ODDS=2.6498;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=224;QR=721;RO=18;RPL=1;RPP=8.80089;RPPR=33.8935;RPR=5;RUN=1;SAF=5;SAP=8.80089;SAR=1;SRF=9;SRP=3.0103;SRR=9;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:18,6:18:721:6:224:0,-4.93423,-4.13712
Chr1    10000534    .   G   A   0.023521    .   AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=8.80089;EPPR=3.94093;GTI=0;LEN=1;MEANALT=1;MQM=5;MQMR=4.09524;NS=1;NUMALT=1;ODDS=5.21571;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=238;QR=836;RO=21;RPL=0;RPP=16.0391;RPPR=40.3389;RPR=6;RUN=1;SAF=5;SAP=8.80089;SAR=1;SRF=11;SRP=3.1137;SRR=10;TYPE=snp    GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:21,6:21:836:6:238:0,-5.37851,-5.02992
Chr1    10000550    .   G   A   22.2538 .   AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=3.0103;EPPR=8.07707;GTI=0;LEN=1;MEANALT=1;MQM=4.58333;MQMR=4.09524;NS=1;NUMALT=1;ODDS=5.11815;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=441;QR=756;RO=21;RPL=1;RPP=21.1059;RPPR=48.6112;RPR=11;RUN=1;SAF=7;SAP=3.73412;SAR=5;SRF=14;SRP=8.07707;SRR=7;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:21,12:21:756:12:441:0,-4.94279,-2.71759
Chr1    10000693    .   C   T   0   .   AB=0;ABP=0;AC=0;AF=0;AN=2;AO=18;CIGAR=1X;DP=85;DPB=85;DPRA=0;EPP=3.0103;EPPR=5.63551;GTI=0;LEN=1;MEANALT=1;MQM=6.5;MQMR=5.86567;NS=1;NUMALT=1;ODDS=58.7168;PAIRED=1;PAIREDR=0.850746;PAO=0;PQA=0;PQR=0;PRO=0;QA=704;QR=2688;RO=67;RPL=6;RPP=7.35324;RPPR=3.30199;RPR=12;RUN=1;SAF=13;SAP=10.7311;SAR=5;SRF=41;SRP=10.3026;SRR=26;TYPE=snp   GT:DP:AD:RO:QR:AO:QA:GL 0/0:85:67,18:67:2688:18:704:0,-16.3647,-26.1838
Chr1    10001052    .   G   A   0.00117747  .   AB=0;ABP=0;AC=0;AF=0;AN=2;AO=24;CIGAR=1X;DP=76;DPB=76;DPRA=0;EPP=3.37221;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=4.91667;MQMR=3.42308;NS=1;NUMALT=1;ODDS=8.21281;PAIRED=0.958333;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=935;QR=2037;RO=52;RPL=13;RPP=3.37221;RPPR=5.68288;RPR=11;RUN=1;SAF=8;SAP=8.80089;SAR=16;SRF=16;SRP=19.7139;SRR=36;TYPE=snp   GT:DP:AD:RO:QR:AO:QA:GL 0/0:76:52,24:52:2037:24:935:0,-12.2127,-5.37127
galaxy vcf gt freebayes • 133 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 4 months ago by deepti1rao10
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

No filtering criteria were set (why the FILTER value is .). This results in all calls being reported in the output whether they are meaningful or not.

You can tune this filtering within Freebayes or filter the VCF results after. The full set of Freebayes options are available on the tool form. Using all defaults is unlikely to give useful results.

Please see the Galaxy Variant Analysis tutorials for example usage of Freebayes and VCF manipulation tools: https://galaxyproject.org/learn/

VCF format: https://samtools.github.io/hts-specs/VCFv4.2.pdf

Freebayes Google group: https://groups.google.com/forum/#!forum/freebayes

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
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