M2 and GDBI for PON: [E::vcf_parse_format] Invalid character '.' in 'AF' FORMAT field at chr1:16949

manolismanolis Member ✭✭

GATK 4.1.1.0, local linux server

Hi,

I ran some WES normal samples:

${gatk} Mutect2 \
-R ${hg38} \
-I "${sample}.bam" \ 
-O "${sample}.vcf.gz" \
-L ${interval} \
-ip 5 \
--max-mnp-distance 0

and then GenomicsDBImport:

${gatk} GenomicsDBImport \
-R ${hg38} \
-V "${sample1}.vcf.gz" \
-V "${sample2}.vcf.gz" \
--batch-size 1 --reader-threads 1 \
--genomicsdb-workspace-path "GDBI_pon" \
-L chr1

Here the error:

13:18:45.329 INFO  GenomicsDBImport - Done initializing engine
13:18:45.517 INFO  GenomicsDBImport - Vid Map JSON file will be written to /home/manolis/prove/GDBI_pon/GDBI_pon/vidmap.json
13:18:45.517 INFO  GenomicsDBImport - Callset Map JSON file will be written to /home/manolis/prove/GDBI_pon/GDBI_pon/callset.json
13:18:45.517 INFO  GenomicsDBImport - Complete VCF Header will be written to /home/manolis/prove/GDBI_pon/GDBI_pon/vcfheader.vcf
13:18:45.517 INFO  GenomicsDBImport - Importing to array - /home/manolis/prove/GDBI_pon/GDBI_pon/genomicsdb_array
13:18:45.517 INFO  ProgressMeter - Starting traversal
13:18:45.517 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Batches Processed   Batches/Minute
13:18:45.820 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
[E::vcf_parse_format] Invalid character '.' in 'AF' FORMAT field at chr1:14653
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fe721be816b, pid=12942, tid=0x00007fe7801f7700
#
# JRE version: OpenJDK Runtime Environment (8.0_152-b12) (build 1.8.0_152-release-1056-b12)
# Java VM: OpenJDK 64-Bit Server VM (25.152-b12 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [libtiledbgenomicsdb8166440819035845683.so+0x35416b]  bcf_unpack+0x36b
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/manolis/prove/GDBI_pon/hs_err_pid12942.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.

Here the header of the vcf.gz and the variant:

##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">

chr1    14653   .   C   T   .   .   DP=13;ECNT=2;MBQ=20,30;MFRL=212,211;MMQ=43,33;MPOS=40;POPAF=7.30;TLOD=10.18 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:9,4:0.333:13:6,2:3,1:0|1:14653_C_T:14653:5,4,3,1

Here the vcf validation:

${gatk} ValidateVariants \
-R ${hg38} \
-V "${sample1}.vcf.gz" \
-L ${interval} \
-ip 5

No any warning ...

When I process the "${sample1}.vcf.gz" with:

bcftools annotate -x FORMAT/AF "${sample1}.vcf.gz" -O z -o "${sample1}_noAF.vcf.gz"

and then running GenomicsDBImport I do not have any error ...

Any suggestion please?
Many thanks

Answers

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