GenotypeGVCFs empty vcf (only headers)

I want to use the joint genotyper (“GenotypeGVCFs” command) to call variants and genotypes for five different samples for which I previously obtained the corresponding g.vcf files. The command that I am using is the following:

java -Xmx64g -jar GenomeAnalysisTK.jar \
-T GenotypeGVCFs \
-R myReferenceSequence.fasta\
-o jointGenotyperSNPs.vcf \
-nt 23 \
-V sample1.final.variants.g.vcf \
-V sample2.final.variants.g.vcf \
-V sample3.final.variants.g.vcf \
-V sample4.final.variants.g.vcf \
-V sample5.final.variants.g.vcf

Unfortunately, the command produces an empty vcf file (only the headers are present).

Any idea why?

Here, the first five rows for each of the samples:

sample1.final.variants.g.vcf
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RS16
cruralis_HybSeqProbes_test_with400Ns_beginend 1 . N . . END=400 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
cruralis_HybSeqProbes_test_with400Ns_beginend 401 . A . . END=410 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,39
cruralis_HybSeqProbes_test_with400Ns_beginend 411 . A . . END=411 GT:DP:GQ:MIN_DP:PL 0/0:2:0:2:0,0,0
cruralis_HybSeqProbes_test_with400Ns_beginend 412 . A . . END=412 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,38
cruralis_HybSeqProbes_test_with400Ns_beginend 413 . A . . END=413 GT:DP:GQ:MIN_DP:PL 0/0:2:0:2:0,0,0

sample2.final.variants.g.vcf
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RS17
cruralis_HybSeqProbes_test_with400Ns_beginend 1 . N . . END=977 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
cruralis_HybSeqProbes_test_with400Ns_beginend 978 . T . . END=1046 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,16
cruralis_HybSeqProbes_test_with400Ns_beginend 1047 . A . . END=1080 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
cruralis_HybSeqProbes_test_with400Ns_beginend 1081 . T . . END=1116 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,18
cruralis_HybSeqProbes_test_with400Ns_beginend 1117 . T . . END=1125 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,32

sample3.final.variants.g.vcf
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RS21
cruralis_HybSeqProbes_test_with400Ns_beginend 1 . N . . END=400 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
cruralis_HybSeqProbes_test_with400Ns_beginend 401 . A . . END=410 GT:DP:GQ:MIN_DP:PL 0/0:3:9:3:0,9,59
cruralis_HybSeqProbes_test_with400Ns_beginend 411 . A . . END=413 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,11
cruralis_HybSeqProbes_test_with400Ns_beginend 414 . A . . END=420 GT:DP:GQ:MIN_DP:PL 0/0:4:6:4:0,6,90
cruralis_HybSeqProbes_test_with400Ns_beginend 421 . C . . END=421 GT:DP:GQ:MIN_DP:PL 0/0:2:0:2:0,0,0

sample4.final.variants.g.vcf
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RS22
cruralis_HybSeqProbes_test_with400Ns_beginend 1 . N . . END=400 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
cruralis_HybSeqProbes_test_with400Ns_beginend 401 . A . . END=406 GT:DP:GQ:MIN_DP:PL 0/0:3:9:3:0,9,57
cruralis_HybSeqProbes_test_with400Ns_beginend 407 . A . . END=410 GT:DP:GQ:MIN_DP:PL 0/0:3:3:3:0,3,45
cruralis_HybSeqProbes_test_with400Ns_beginend 411 . A . . END=411 GT:DP:GQ:MIN_DP:PL 0/0:3:0:3:0,0,21
cruralis_HybSeqProbes_test_with400Ns_beginend 412 . A . . END=412 GT:DP:GQ:MIN_DP:PL 0/0:3:3:3:0,3,45

sample5.final.variants.g.vcf
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RS60
cruralis_HybSeqProbes_test_with400Ns_beginend 1 . N . . END=484 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
cruralis_HybSeqProbes_test_with400Ns_beginend 485 . T . . END=493 GT:DP:GQ:MIN_DP:PL 0/0:3:9:3:0,9,49
cruralis_HybSeqProbes_test_with400Ns_beginend 494 . G . . END=494 GT:DP:GQ:MIN_DP:PL 0/0:3:0:3:0,0,0
cruralis_HybSeqProbes_test_with400Ns_beginend 495 . A . . END=497 GT:DP:GQ:MIN_DP:PL 0/0:3:9:3:0,9,53
cruralis_HybSeqProbes_test_with400Ns_beginend 498 . T . . END=499 GT:DP:GQ:MIN_DP:PL 0/0:3:0:3:0,0,0

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