limx54 / kggseq Goto Github PK

Dear Li,
Does KGGSEQ could output OR and CI value in gene and set based analysis?

Hello, Mr. Li,
I have used your tool kggseq, and I have a question for it. I really look forward to your answer！
I have a series of WES vcf documents for 20 patients, and I want to use kggseq to find which variants are pathogenic. So I run the following command：
java -jar kggseq.jar --vcf-file /Users/zhouzhiyuan/Desktop/yang实验/FLG/第二次检测_海普洛斯胚系检测20例/Result/HGC20210303005_20210330/Result/04.Mutation/SNV_INDEL/A10_snp.vcf --indiv-pheno A10:2 --db-score dbnsfp --mendel-causing-predict best --filter-nondisease-variant

When I run it, it returns the following results:
com.esotericsoftware.kryo.KryoException: java.util.zip.ZipException: invalid stored block lengths
Serialization trace:
customizedGeneAnnot (org.cobi.kggseq.entity.Variant)
at com.esotericsoftware.kryo.io.Input.fill(Input.java:185)
at com.esotericsoftware.kryo.io.Input.require(Input.java:216)
at com.esotericsoftware.kryo.io.Input.readVarIntFlag(Input.java:480)
at com.esotericsoftware.kryo.io.Input.readString(Input.java:775)
at com.esotericsoftware.kryo.serializers.DefaultSerializers$StringSerializer.read(DefaultSerializers.java:165)
at com.esotericsoftware.kryo.serializers.DefaultSerializers$StringSerializer.read(DefaultSerializers.java:155)
at com.esotericsoftware.kryo.serializers.DeflateSerializer.read(DeflateSerializer.java:67)
at com.esotericsoftware.kryo.Kryo.readObjectOrNull(Kryo.java:773)
at com.esotericsoftware.kryo.serializers.ReflectField.read(ReflectField.java:120)
at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:122)
at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:696)
at org.cobi.kggseq.entity.Genome.loadVariantFromDisk(Unknown Source)
at org.cobi.kggseq.NewCUIApp.process(Unknown Source)
at org.cobi.kggseq.NewCUIApp.main(Unknown Source)
Caused by: java.util.zip.ZipException: invalid stored block lengths
at java.base/java.util.zip.InflaterInputStream.read(InflaterInputStream.java:164)
at com.esotericsoftware.kryo.io.Input.fill(Input.java:183)
... 13 more

And it returns 0 variant.
I’m wondering where the mistake is, and whether this command line is appropriate for detecting pathogenic variants from a vcf document for cancer (nasopharyngeal carcinoma). I am really appreciated for your answer!!