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weird lines when calling variants with GATK, this might be a common issue

purodpurod Member
edited May 2019 in Ask the GATK team

I called variants and some lines are weird in the output g.vcf file

chr05 9723222 . A C, 1013.03 . DP=21;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=61996,21 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,21,0:21:69:0|1:9723222_A_C:1027,69,0,1027,69,1027:9723222:0,0,15,6

The weird part is in bold format. Did anyone get the same problem as me?

Best Answer


  • bshifawbshifaw Member, Broadie, Moderator admin

    Hi @purod

    What command did you use and what version of GATK are you using?


  • purodpurod Member

    The GATK version is and the command is

    First step: gatk HaplotypeCaller -R /work7_P1/GATK_RegionCall/IRGSP-1.0/IRGSP-1.0_genome.fasta -I /work7_P1/GATK_RegionCall/Bam_SortIndex/B001.g.vcf -O /work7_P1/GATK_RegionCall/Variant_call/B001.g.vcf -L /work7_P1/GATK_RegionCall/IRGSP-1.0/reduce.list -ERC GVCF --max-alternate-alleles 25 [reduce.list is the region I would like to call variants]

    Second step: gatk GenomicsDBImport --sample-name-map /work7_P1/GATK_RegionCall/Variant_call/cohort.sample_map --reader-threads 5 --batch-size 50 --genomicsdb-workspace-path /work7_P1/GATK_RegionCall/DBimport/chr01_directory --intervals chr01

    Third step: gatk GenotypeGVCFs -R /work7_P1/GATK_RegionCall/IRGSP-1.0/IRGSP-1.0_genome.fasta -V gendb:///work7_P1/GATK_RegionCall/DBimport/chr01_directory -O /work7_P1/GATK_RegionCall/Geno_call/chr01_output.vcf

    Rerun the code might remove this error. However, I got thousands of files and if this is a random error, I have to rerun again and again. I also suspect the name of chromosome causing this error, maybe I should use just the number instead of chr01. Totally have no idea what causes this. I really appreciate if you can figure this out.

  • purodpurod Member
    Accepted Answer

    The information comes from PGT tag, I can ask GATK not to output this with option "--doNotRunPhysicalPhasing"

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