Hello!
I have used varscan in order to call my variants,now I would like filter they using frequency,
So I have tried snpsift, with this command:
java -jar SnpSift.jar filter "(GEN[*].FREQ>20)" midvarScan1.snp.vcf.gz > output
But my file in empty.
This a sample of my file:
Could you help me?
Thank you very much
I have used varscan in order to call my variants,now I would like filter they using frequency,
So I have tried snpsift, with this command:
java -jar SnpSift.jar filter "(GEN[*].FREQ>20)" midvarScan1.snp.vcf.gz > output
But my file in empty.
This a sample of my file:
Code:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 chr13 32893198 . T G . PASS ADP=58;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:73:58:58:13:19:50%:3,9837E-8:25:26:12:1:0:19 chr13 32900364 . T C . PASS ADP=166;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:101:166:166:72:30:26,32%:7,608E-11:23:23:52:20:11:19 chr13 32900607 . A T . PASS ADP=121;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:162:121:121:70:46:39,66%:5,2238E-17:26:25:66:4:0:46 chr13 32903685 . C T . PASS ADP=143;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:193:143:143:88:55:38,46%:4,2774E-20:27:27:48:40:36:19 chr13 32912299 . T C . PASS ADP=279;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:255:279:279:161:117:41,94%:9,8413E-43:28:27:58:103:46:71 chr13 32913055 . A G . PASS ADP=289;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:289:289:0:288:99,65%:1,2167E-172:0:27:0:0:137:151 chr13 32915005 . G C . PASS ADP=56;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:56:56:0:56:100%:2,5602E-33:0:28:0:0:28:28 chr13 32929387 . T C . PASS ADP=173;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:173:173:0:173:100%:1,6275E-103:0:28:0:0:55:118 chr13 32931852 . T C . PASS ADP=84;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:53:84:84:43:16:26,23%:4,7113E-6:25:26:33:10:7:9 chr13 32936646 . T C . PASS ADP=99;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:174:99:99:49:47:47,96%:3,6959E-18:27:27:35:14:31:16
Thank you very much
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