Question: Question about FreeBayes output
0
gravatar for sv67
6 months ago by
sv670
sv670 wrote:

Hi

I just completed a run on Galaxy using SRA data. The vcf file generated after using Freebayes gave me the following:

This is what Galaxy is giving me:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown

NC_000001.11 10045 . ACC ACCC 4.08866 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1M1I2M;DP=2;DPB=2.66667;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=20;MQMR=0;NS=1;NUMALT=1;ODDS=0.445176;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=ins GT:DP:DPR:RO:QR:AO:QA:GL 1/1:2:2,2:0:0:2:22:-1.99952,-0.60206,0 NC_000001.11 49298 . T C 466.836 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=41;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=92.0407;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=23;MQMR=0;NS=1;NUMALT=1;ODDS=60.3446;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1393;QR=0;RO=0;RPL=41;RPP=92.0407;RPPR=0;RPR=0;RUN=1;SAF=41;SAP=92.0407;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 1/1:41:41,41:0:0:41:1393:-83.7103,-12.3422,0 NC_000001.11 55085 . T A 25.4964 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=23;MQMR=0;NS=1;NUMALT=1;ODDS=5.86606;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 1/1:2:2,2:0:0:2:80:-4.35378,-0.60206,0 NC_000001.11 414577 . A G 24.6657 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=23;MQMR=0;NS=1;NUMALT=1;ODDS=5.67419;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=64;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 1/1:2:2,2:0:0:2:64:-4.27045,-0.60206,0 NC_000001.11 414665 . C T 5.81606 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=23;MQMR=0;NS=1;NUMALT=1;ODDS=1.03344;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=25;QR=0;RO=0;RPL=2;RPP=7.35324;RPPR=0;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 1/1:2:2,2:0:0:2:25:-2.255,-0.60206,0

But I don;t see any mapping to rd-ids. I am looking for something like this: This is the correct format that I want

fileformat=VCFv4.0

FILTER=<id=abfilter,description="ab &gt;="" 0.75"="">

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 6001 6002 6003 6004 6005 6006 6007 6008

1 985900 rs17160776 C T 456.91 PASS AB=0.44;AC=1;AF=0.063;AN=16;BaseQRankSum=20.401;DB;Dels=0.00;HRun=2;HaplotypeScore=0.0831;MQ=60.00;MQ0=0;MQRankSum=3.060;QD=16.92;ReadPosRankSum=4.731;SB=-165.72 GT:AD:DP:GQ:PL 0/0:18,0:18:54.17:0,54,660 0/0:18,0:18:54.15:0,54,664 0/0:20,0:20:60.17:0,60,726 0/0:20,0:20:57.17:0,57,679 0/0:24,0:24:72.20:0,72,871 0/1:12,15:27:99:496,0,358 0/0:9,0:9:27.08:0,27,318 0/0:30,0:30:90.28:0,90,1120 3 39135551 rs17852414 G A 4602.20 PASS AB=0.52;AC=2;AF=0.125;AN=16;BaseQRankSum=88.308;DB;Dels=0.00;HRun=1;HaplotypeScore=0.4329;MQ=59.94;MQ0=0;MQRankSum=7.295;QD=18.86;ReadPosRankSum=8.891;SB=-664.50 GT:AD:DP:GQ:PL 0/0:122,0:122:99:0,367,4861 0/0:107,0:107:99:0,322,4242 0/0:112,0:112:99:0,337,4512 0/1:67,61:128:99:2013,0,2237 0/0:110,0:110:99:0,328,4279 0/1:60,56:116:99:1860,0,1977 0/0:142,0:142:99:0,412,5520 0/0:125,0:125:99:0,376,5026 4 22820504 rs358231 A T 38634.61 PASS AB=0.48;AC=14;AF=0.875;AN=16;BaseQRankSum=200.000;DB;Dels=0.00;HRun=0;HaplotypeScore=2.4533;MQ=59.93;MQ0=0;MQRankSum=4.366;QD=33.77;ReadPosRankSum=11.467;SB=-12956.00 GT:AD:DP:GQ:PL 1/1:0,155:155:99:5990,467,0 1/1:0,125:126:99:4824,373,0 1/1:0,162:162:99:6262,488,0 1/1:1,143:144:99:5431,427,0 0/1:59,74:133:99:2481,0,1910 1/1:0,132:132:99:5089,394,0 0/1:80,76:156:99:2419,0,2672 1/1:0,135:136:99:5216,403,0

Any help will be greatly appreciated.

Thanks!

sra variant vcf galaxy freebayes • 191 views
ADD COMMENTlink written 6 months ago by sv670
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