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GenotypeGVCFs: no records in VCF
Dear GATK team,
I am having troubles calling genotypes on
*.gvcf produced by
HaplotypeCaller in GVCF mode.
When I run
GenotypeGVCFs (GATK 3.5), I get only header in resulting VCF file, but no records.
I had no such problem before.
Could you advice on possible reason of the issue and how to fix it?
Here is the command and output:
java -Xmx12g -Djava.io.tmpdir=./tmp -jar GenomeAnalysisTK.jar \ -T GenotypeGVCFs \ -R reference.fa \ --variant sample1.g.vcf \ --variant sample2.g.vcf \ --variant sample3.g.vcf \ --variant sample4.g.vcf --variant sample5.g.vcf --variant sample6.g.vcf --variant sample7.g.vcf --variant sample7.g.vcf \ --num_threads 4 \ -o TEST.gt.vcf
note: there are SNPs/INDELs in
##fileformat=VCFv4.2 ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> ##FILTER=<ID=LowQual,Description="Low quality"> ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)"> ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> ... ... ... #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8