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Picard LiftoverVcf changes the . (dot) value into PASS for the FILTER field in a VCF file.

dw15dw15 Member
edited December 2018 in Ask the GATK team
I'm using Picard (version 2.18.11) LiftoverVcf to lift VCF files from hg19 to b37.
command I used is:

picard LiftoverVcf I=raw_variants_merged_1543959099.0026_chrm_filtered.vcf O=raw_variants_merged_1543959099.0026_chrm_filtered_b37.vcf CHAIN=Liftover_Chain_Files/hg19tob37.chain REJECT=raw_variants_merged_1543959099.0026_chrm_filtered_rejected_hg19tob37.vcf R=human_g1k_v37.fasta

After lifting, I found that all the . (dots) in the FILTER field of the original VCF file are changed to PASS , while the other FILTER values stay the same after lifting.

Any one encountered the same issue? How do I keep the original FILTER values when I use the LiftoverVcf ?



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