I always appreciate you.
I obtained funcotator_dataSources.v1.6.20190124s.tar.gz to use funcotator using a below command.
The chromosme names were coded as chr1, chr2, chr3, chr4, ... in the file funcotator_dataSources.v1.6.20190124s/dbsnp/hg19/hg19_All_20170710.vcf.gz.
However, I noticed that the chromosme names were coded as 1,2, 3, 4, ... in the file funcotator_dataSources.v1.6.20190124s/dbsnp/hg38/hg38_All_20170710.vcf.gz.
Could you correct it in the hg38 dbSNP file?
Can you please provide
a) GATK version used : 22.214.171.124
b) Exact GATK commands used :
java -Xmx5g -jar gatk-package-126.96.36.199-local.jar FuncotatorDataSourceDownloader --somatic --validate-integrity --extract-after-download
c) The entire error log if applicable.
Please sign in to leave a comment.