Hi,
I am trying to filter vcf files that were previously annotated using snpsift dbsnfp.
A typical line with the annotations looks like:
chr20 256727 rs3827147 T A 999.0 . DP=2287;VDB=3.180612e-02;RPB=2.176635e+00;AF1=0.5;G3=5.969e-50,1,5e-52;HWE=1.4e-07;AC1=20;DP4=724,698,499,366;MQ=44;FQ=999;PV4=0.0018,1,4.8e-66,1;EFF=DOWNSTREAM(MODIFIER||483||C20orf96|protein_coding|CODING|ENST00000400269|),INTRAGENIC(MODIFIER||||C20orf96||CODING||),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I270F|C20orf96|protein_coding|CODING|ENST00000382369|8),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I305F|C20orf96|protein_coding|CODING|ENST00000360321|10),SPLICE_SITE_REGION(LOW||||C20orf96|protein_coding|CODING|ENST00000360321|10),SPLICE_SITE_REGION(LOW||||C20orf96|protein_coding|CODING|ENST00000382369|8);dbNSFP_GERP++_RS=-1.09;dbNSFP_1000Gp1_ASN_AF=0.701048951048951;dbNSFP_Uniprot_acc=Q9NUD7|Q5JYC3;dbNSFP_MutationTaster_pred=P;dbNSFP_ESP6500_AA_AF=0.726736;dbNSFP_29way_logOdds=3.58;dbNSFP_SIFT_pred=T;dbNSFP_Polyphen2_HDIV_pred=B|B;dbNSFP_1000Gp1_AFR_AF=0.7378048780487805;dbNSFP_1000Gp1_EUR_AF=0.6437994722955145;dbNSFP_ESP6500_EA_AF=0.617442;dbNSFP_LRT_pred=N;dbNSFP_1000Gp1_AMR_AF=0.5027624309392266;dbNSFP_GERP++_NR=4.7;dbNSFP_1000Gp1_AF=0.6565934065934066;dbNSFP_Polyphen2_HVAR_pred=B|B;PhastCons=0.098 GT:PL
P:SP:GQ 0/1:255,0,255:89:6:99 0/1:255,0,255:65:2:99 0/1:232,0,255:38:8:99 0/1:255,0,255:190:8:99 0/1:255,0,255:229:3:99 0/1:255,0,255:186:4:99 0/1:255,0,255:127:3:99 0/1:255,0,255:128:1:99 0/1:255,0,255:156:9:99 0/1:255,0,255:85:4:99 0/1:255,0,255:84:8:99 0/1:255,0,255:157:10:99 0/1:255,0,255:102:27:99 0/1:255,0,255:91:1:99 0/1:255,0,255:84:6:99 0/1:255,0,255:56:1:99 0/1:255,0,255:57:4:99 0/1:255,0,255:135:4:99 0/1:255,0,255:127:3:99 0/1:255,0,255:101:4:99
Now I would like to filter the resulting vcf based on the predicted effect of the variant according to SIFT and PolyPhen2. I tried
java -jar SnpSift.jar filter "(exists dbNSFP_SIFT_pred)" -f chr20.vcf
which returns an empty vcf file.
I also tried
java -jar SnpSift.jar filter "(dbNSFP_SIFT_pred='D')" -f chr20.vcf
However this resuts in a java error:
Exception in thread "main" java.lang.RuntimeException: Unknow return type 'Character'
at ca.mcgill.mcb.pcingola.snpSift.lang.expression.Field.get(Field.java:62)
at ca.mcgill.mcb.pcingola.snpSift.lang.expression.Expression.canCompareTo(Expression.java:20)
at ca.mcgill.mcb.pcingola.snpSift.lang.condition.Eq.eval(Eq.java:20)
at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.evaluate(SnpSiftCmdFilter.java:191)
at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:356)
at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:322)
at ca.mcgill.mcb.pcingola.snpSift.SnpSift.run(SnpSift.java:233)
at ca.mcgill.mcb.pcingola.snpSift.SnpSift.main(SnpSift.java:60)
So it seems that the filter itself (the way I construct it) is not recognizable by the program.
Anybody has any idea what I am doing wrong hear and how to apply this and similar filters?
Thanks in advance for any help
I am trying to filter vcf files that were previously annotated using snpsift dbsnfp.
A typical line with the annotations looks like:
chr20 256727 rs3827147 T A 999.0 . DP=2287;VDB=3.180612e-02;RPB=2.176635e+00;AF1=0.5;G3=5.969e-50,1,5e-52;HWE=1.4e-07;AC1=20;DP4=724,698,499,366;MQ=44;FQ=999;PV4=0.0018,1,4.8e-66,1;EFF=DOWNSTREAM(MODIFIER||483||C20orf96|protein_coding|CODING|ENST00000400269|),INTRAGENIC(MODIFIER||||C20orf96||CODING||),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I270F|C20orf96|protein_coding|CODING|ENST00000382369|8),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I305F|C20orf96|protein_coding|CODING|ENST00000360321|10),SPLICE_SITE_REGION(LOW||||C20orf96|protein_coding|CODING|ENST00000360321|10),SPLICE_SITE_REGION(LOW||||C20orf96|protein_coding|CODING|ENST00000382369|8);dbNSFP_GERP++_RS=-1.09;dbNSFP_1000Gp1_ASN_AF=0.701048951048951;dbNSFP_Uniprot_acc=Q9NUD7|Q5JYC3;dbNSFP_MutationTaster_pred=P;dbNSFP_ESP6500_AA_AF=0.726736;dbNSFP_29way_logOdds=3.58;dbNSFP_SIFT_pred=T;dbNSFP_Polyphen2_HDIV_pred=B|B;dbNSFP_1000Gp1_AFR_AF=0.7378048780487805;dbNSFP_1000Gp1_EUR_AF=0.6437994722955145;dbNSFP_ESP6500_EA_AF=0.617442;dbNSFP_LRT_pred=N;dbNSFP_1000Gp1_AMR_AF=0.5027624309392266;dbNSFP_GERP++_NR=4.7;dbNSFP_1000Gp1_AF=0.6565934065934066;dbNSFP_Polyphen2_HVAR_pred=B|B;PhastCons=0.098 GT:PL
P:SP:GQ 0/1:255,0,255:89:6:99 0/1:255,0,255:65:2:99 0/1:232,0,255:38:8:99 0/1:255,0,255:190:8:99 0/1:255,0,255:229:3:99 0/1:255,0,255:186:4:99 0/1:255,0,255:127:3:99 0/1:255,0,255:128:1:99 0/1:255,0,255:156:9:99 0/1:255,0,255:85:4:99 0/1:255,0,255:84:8:99 0/1:255,0,255:157:10:99 0/1:255,0,255:102:27:99 0/1:255,0,255:91:1:99 0/1:255,0,255:84:6:99 0/1:255,0,255:56:1:99 0/1:255,0,255:57:4:99 0/1:255,0,255:135:4:99 0/1:255,0,255:127:3:99 0/1:255,0,255:101:4:99Now I would like to filter the resulting vcf based on the predicted effect of the variant according to SIFT and PolyPhen2. I tried
java -jar SnpSift.jar filter "(exists dbNSFP_SIFT_pred)" -f chr20.vcf
which returns an empty vcf file.
I also tried
java -jar SnpSift.jar filter "(dbNSFP_SIFT_pred='D')" -f chr20.vcf
However this resuts in a java error:
Exception in thread "main" java.lang.RuntimeException: Unknow return type 'Character'
at ca.mcgill.mcb.pcingola.snpSift.lang.expression.Field.get(Field.java:62)
at ca.mcgill.mcb.pcingola.snpSift.lang.expression.Expression.canCompareTo(Expression.java:20)
at ca.mcgill.mcb.pcingola.snpSift.lang.condition.Eq.eval(Eq.java:20)
at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.evaluate(SnpSiftCmdFilter.java:191)
at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:356)
at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:322)
at ca.mcgill.mcb.pcingola.snpSift.SnpSift.run(SnpSift.java:233)
at ca.mcgill.mcb.pcingola.snpSift.SnpSift.main(SnpSift.java:60)
So it seems that the filter itself (the way I construct it) is not recognizable by the program.
Anybody has any idea what I am doing wrong hear and how to apply this and similar filters?
Thanks in advance for any help