The order of file Mills_and_1000G_gold_standard.indels.hg38.vcf is not same with my genome fasta file,so I need to reorder it,I use SortVcf to do it.Before I run it,I run UpdateVcfSequenceDictionary first.My scripts is as follows:
java -jar /data/share-disk/kvm72/yangzhen/programe/picard.jar UpdateVcfSequenceDictionary \
I=Mills_and_1000G_gold_standard_rename.indels.hg38.vcf \
O=Mills_and_1000G_gold_standard_dict.indels.hg38.vcf \
SEQUENCE_DICTIONARY=/data2/gminix/pipeline/toolkits/RNA_seq_SNP-INDEL/data/hg38v1.dict
java -jar /data/share-disk/kvm72/yangzhen/programe/picard.jar SortVcf \
I=Mills_and_1000G_gold_standard_dict.indels.hg38.vcf \
O=Mills_and_1000G_gold_standard_reorder.indels.hg38.vcf \
SEQUENCE_DICTIONARY=/data2/gminix/pipeline/toolkits/RNA_seq_SNP-INDEL/data/hg38v1.dict
It didn't give any error,but just counld not finish it.The report is shown in the picture:
It stops there and no longer runs,what can be the problem?
java -jar /data/share-disk/kvm72/yangzhen/programe/picard.jar UpdateVcfSequenceDictionary \
I=Mills_and_1000G_gold_standard_rename.indels.hg38.vcf \
O=Mills_and_1000G_gold_standard_dict.indels.hg38.vcf \
SEQUENCE_DICTIONARY=/data2/gminix/pipeline/toolkits/RNA_seq_SNP-INDEL/data/hg38v1.dict
java -jar /data/share-disk/kvm72/yangzhen/programe/picard.jar SortVcf \
I=Mills_and_1000G_gold_standard_dict.indels.hg38.vcf \
O=Mills_and_1000G_gold_standard_reorder.indels.hg38.vcf \
SEQUENCE_DICTIONARY=/data2/gminix/pipeline/toolkits/RNA_seq_SNP-INDEL/data/hg38v1.dict
It didn't give any error,but just counld not finish it.The report is shown in the picture:
It stops there and no longer runs,what can be the problem?