where can i download small_exac_common_3_hg19.vcf and idx file for GATK GetPileupSummaries

Question

[zhao03]

Hi, where can i download small_exac_common_3_hg19.vcf and idx file for GATK GetPileupSummaries ? the web only support hg38,ftp://ftp.broadinstitute.org/bundle/ thank you!

Answer 1

[zhao03]

i have got it. picard can transport the b37 to hg19. java -Xmx6g -jar /home/D/ref/picard/picard.jar LiftoverVcf \ I=small_exac_common_3_b37.vcf \ O=small_exac_common_3_hg19.vcf CHAIN=b37tohg19.chain REJECT=rejected_variants.vcf R=/home/D/ref/hg19/ucsc.hg19.fasta