Attention:
The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.

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 ?

Thanks,
Dongjing

Answers

Sign In or Register to comment.