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Nilmini

Hello GATK team,

I am having some trouble at the jointgenotyping step. Any assistance is appreciated

- I am using GATK 4.1.0.0.
- I have 10 samples, for which I used Haplotypecaller individually in GVCF mode, to create 10 GVCF files.
- Then I tried combining these files with CombineGVCF, which produced a 12GB file, I assume this file has the 10 GVCF's combined (cohort.g.vcf.gz).

command used-
gatk CombineGVCFs -R bowhead_scaffolds_ref.fasta --variant In1.g.vcf.gz --variant In3.g.vcf.gz --variant In4.g.vcf.gz --variant In5.g.vcf.gz --variant In6.g.vcf.gz --variant In7.g.vcf.gz --variant In8.g.vcf.gz --variant In9.g.vcf.gz --variant In10.g.vcf.gz -O cohort.g.vcf.gz


- Then I tried using GenotypeGVCF on the cohort.g.vcf.gz

command used-
gatk GenotypeGVCFs -R bowhead_scaffolds_ref.fasta -V cohort.g.vcf.gz -O output.vcf.gz



-which created a vcf file, but this vcf file had only one column with genotype (I expected to see a flat vcf file with the 10 individuals I have [the normal standard joint vcf format, should have all 10 individuals with their genotypes and other info init])


This is what my vcf output from GATK looks like

##source=CombineGVCFs
##source=GenotypeGVCFs
##source=HaplotypeCaller
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bar
scaffold_4215 134 . C T 96.80 . AC=2;AF=1.00;AN=2;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.76;QD=32.27;SOR=2.833 GT:AD:DP:GQ:PL 1/1:0,3:3:9:110,9,0
scaffold_4215 406 . T G 158.10 . AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.36;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,4:4:12:172,12,0
scaffold_4215 634 . T C 388.01 . AC=2;AF=1.00;AN=2;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.73;SOR=1.402 GT:AD:DP:GQ:PL 1/1:0,9:9:27:402,27,0
scaffold_4215 858 . C T 197.92 . AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.97;SOR=1.981 GT:AD:DP:GQ:PL 1/1:0,5:5:15:212,15,0
scaffold_4215 961 . A C 118.80 . AC=2;AF=1.00;AN=2;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=27.24;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,3:3:9:132,9,0
scaffold_4215 1880 . G A 182.93 . AC=2;AF=1.00;AN=2;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.49;SOR=1.329 GT:AD:DP:GQ:PL 1/1:0,6:6:18:197,18,0

What could be the reason for this? and is any one of these tools are not working properly?

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