LiftOverVCF¶
module load picard/2.9.4
java -jar /hpcf/apps/picard/install/2.9.4/picard.jar LiftoverVcf I=hbf.annotated.noSamples.epi.vcf.gz O=hbf.annotated.noSamples.epi.hg19.vcf.gz CHAIN=~/Data/chain_files/hg38ToHg19.over.chain.gz REJECT=rejected_variants.vcf R=~/Data/Human/hg19/fasta/samtools/hg19.fa
I found picard/2.21.2 has problem.
300MB vcf gz needs about 20G memory, very fast, 4 min
sub-set vcf¶
=cut vcf 1
# this program doesn't require much memory
ncore=1
mem=4000
q=rhel7_priority
module load vcftools/0.1.16
vcftools --gzvcf sgp884.snpEff.gnomad.clinvar.LanceAnno.vcf.gz --recode-INFO-all --out sgp884.snpEff.gnomad.clinvar.LanceAnno.loci.vcf --recode --bed loci.bed
ref¶
https://www.biostars.org/p/46331/