I'm hoping someone may have some pearls of wisdom. I've been trying to liftover .vcf files (human) from build 37 to build 38, and have tried a variety of different approaches, none of which have worked so far. NCBI's web tool produces an error stating that I am trying to access a page I do not have access to (despite using their own web submission form to submit the .vcf.gz file!), I keep receiving a gateway time-out error from Ensembl's genome assembly tool, and Picard's LiftoverVcf program produces the following null pointer exception errors:
java -jar picard.jar LiftoverVcf I=Input.vcf O=Output.vcf CHAIN=hg19ToHg38.over.chain REJECT=rejected_variants_chr22.vcf R=hg38.fa
Exception in thread "main" java.lang.NullPointerException at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:218) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:268) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)
Does anyone have any suggestions for an approach that may be more successful than the above? Or any fixes for these issues?
Thank you very much in advance for any suggestions you might have!