Error with SNPSift while using dbNSFP2.9.txt.gz for annotation
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7.3 years ago
always_learning ★ 1.1k

Dear All,

I have been using SNPSift for annotating VCF with database dbNSFPv_2.6.txt.gz and its working perfectly. Now I am using SNPSift with dbNSFP2.9.txt.gz version for few other annotation like ExAC frequency but getting Null Pointer exception.

If some one else got same error while trying dbNSFP2.9.txt.gz with SNPSift?

Here is command that I am using and associated errors too.

java -jar /gpfs/software/genomics/snpEff/4.1A/SnpSift.jar dbnsfp -v -db /gpfs/data_jrnas1/ref_data/Hsaens/GRCh37/variation/dbNSFP2.9.txt.gz GA_151.GATK.annotated_10000.vcf
00:00:00.000    SnpSift version SnpSift 4.1a (build 2015-01-14), by Pablo Cingolani
00:00:00.003    Command: 'DBNSFP'
00:00:00.003    Reading configuration file 'snpEff.config'
00:00:00.282    done
00:00:00.283    Annotating
    Input file    : 'GA_151.GATK.annotated_10000.vcf'
    Database file : '/gpfs/data_jrnas1/ref_data/Hsapiens/GRCh37/variation/dbNSFP2.9.txt.gz'
Exception in thread "main" java.lang.RuntimeException: java.lang.NullPointerException
    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdDbNsfp.annotate(SnpSiftCmdDbNsfp.java:100)
    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdDbNsfp.run(SnpSiftCmdDbNsfp.java:423)
    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdDbNsfp.run(SnpSiftCmdDbNsfp.java:408)
    at ca.mcgill.mcb.pcingola.snpSift.SnpSift.run(SnpSift.java:360)
    at ca.mcgill.mcb.pcingola.snpSift.SnpSift.main(SnpSift.java:69)
Caused by: java.lang.NullPointerException
    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdDbNsfp.initAnnotate(SnpSiftCmdDbNsfp.java:350)
    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdDbNsfp.annotate(SnpSiftCmdDbNsfp.java:98)
SNPeff Annotation SNP SNPSift • 2.3k views
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