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Old 03-02-2015, 02:12 PM   #4
lindenb
Senior Member
 
Location: France

Join Date: Apr 2010
Posts: 143
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using my tool vcffilterjs: https://github.com/lindenb/jvarkit/wiki/VCFFilterJS

Code:
curl -Ls "https://raw.githubusercontent.com/cs418-familysnps/familysnps/3ab8d34c7a7afd7336a40c8f79a32787dcb01389/SNPPhasingProject/vcf/test/bcftools.vcf" |\
java -jar dist-1.128/vcffilterjs.jar -e 'function accept(v) { if(!v.hasAttribute("DP4")) return false; var tokens=v.getAttribute("DP4"); return tokens.get(2)>0 && tokens.get(3)>0;} accept(variant);'
output:

Code:
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
MT	321	.	T	.	283	.	AC1=0;AF1=0;DP=289;DP4=270,3,1,1;FQ=-282;MQ=56;PV4=0.029,0.00028,0.12,0.0089;VDB=0.0302	PL	0
MT	344	.	T	.	283	.	AC1=0;AF1=0;DP=392;DP4=319,49,1,1;FQ=-282;MQ=55;PV4=0.25,6.8e-05,0.16,1;VDB=0.0394	PL	0
MT	354	.	C	.	283	.	AC1=0;AF1=0;DP=481;DP4=328,104,1,1;FQ=-282;MQ=53;PV4=0.43,0.00091,0.012,1;VDB=0.0447	PL	0
MT	360	.	A	.	283	.	AC1=0;AF1=0;DP=515;DP4=355,125,1,1;FQ=-282;MQ=52;PV4=0.45,2.4e-06,0.29,0.0068;VDB=0.0090	PL	0
MT	366	.	G	.	283	.	AC1=0;AF1=0;DP=553;DP4=385,146,1,2;FQ=-282;MQ=52;PV4=0.19,5.9e-09,0.12,1;VDB=0.0429	PL	0
MT	375	.	C	.	283	.	AC1=0;AF1=0;DP=620;DP4=406,186,7,4;FQ=-282;MQ=51;PV4=0.75,1,0.49,1;VDB=0.0394	PL	0
MT	405	.	T	.	283	.	AC1=0;AF1=0;DP=766;DP4=479,272,1,1;FQ=-282;MQ=51;PV4=1,2.2e-21,1,0.19;VDB=0.0227	PL	0
MT	416	.	T	.	283	.	AC1=0;AF1=0;DP=788;DP4=473,306,1,1;FQ=-282;MQ=52;PV4=1,5.1e-12,0.31,1;VDB=0.0205	PL	0
MT	434	.	C	.	283	.	AC1=0;AF1=0;DP=779;DP4=442,285,3,1;FQ=-282;MQ=53;PV4=1,8.7e-16,1,0.0067;VDB=0.0367	PL	0
MT	450	.	T	.	283	.	AC1=0;AF1=0;DP=758;DP4=446,248,1,1;FQ=-282;MQ=56;PV4=1,0.00099,0.031,0.3;VDB=0.0242	PL	0
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