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Combine GVCFs dropping samples

slg1128slg1128 ConnecticutMember
Hello,

I am trying to run CombineGVCFs on a set of 75 bacterial samples.

I have run all 75 samples through the haplotypecaller pipeline and have GVCFs and index files for all of them. However, when I try to combine these into one GVCF for joint calling two of the samples (JKS2066 and JKS2131) are dropped. They are both included in the command so I am not sure why they are not included in the final GVCF. Is there some parameter I can use to force all GVCFs to be combined?

Command:

module load GATK/4.0
export _JAVA_OPTIONS=-Djava.io.tmpdir=/scratch

gatk CombineGVCFs \
-R JKS2530_filtered_reformat.assembly.fasta \
-V haplotypes_final/JKS1101_haplotype_final.g.vcf \
-V haplotypes_final/JKS1106_haplotype_final.g.vcf \
-V haplotypes_final/JKS1114_haplotype_final.g.vcf \
-V haplotypes_final/JKS1126_haplotype_final.g.vcf \
-V haplotypes_final/JKS1134_haplotype_final.g.vcf \
-V haplotypes_final/JKS1136_haplotype_final.g.vcf \
-V haplotypes_final/JKS1144_haplotype_final.g.vcf \
-V haplotypes_final/JKS1146_haplotype_final.g.vcf \
-V haplotypes_final/JKS1190_haplotype_final.g.vcf \
-V haplotypes_final/JKS1214_haplotype_final.g.vcf \
-V haplotypes_final/JKS1217_haplotype_final.g.vcf \
-V haplotypes_final/JKS2056_haplotype_final.g.vcf \
-V haplotypes_final/JKS2058_haplotype_final.g.vcf \
-V haplotypes_final/JKS2060_haplotype_final.g.vcf \
-V haplotypes_final/JKS2066_haplotype_final.g.vcf \
-V haplotypes_final/JKS2069_haplotype_final.g.vcf \
-V haplotypes_final/JKS2072_haplotype_final.g.vcf \
-V haplotypes_final/JKS2078_haplotype_final.g.vcf \
-V haplotypes_final/JKS2115_haplotype_final.g.vcf \
-V haplotypes_final/JKS2123_haplotype_final.g.vcf \
-V haplotypes_final/JKS2128_haplotype_final.g.vcf \
-V haplotypes_final/JKS2131_haplotype_final.g.vcf \
-V haplotypes_final/JKS2138_haplotype_final.g.vcf \
-V haplotypes_final/JKS2146_haplotype_final.g.vcf \
-V haplotypes_final/JKS2148_haplotype_final.g.vcf \
-V haplotypes_final/JKS2155_haplotype_final.g.vcf \
-V haplotypes_final/JKS2160_haplotype_final.g.vcf \
-V haplotypes_final/JKS2162_haplotype_final.g.vcf \
-V haplotypes_final/JKS2168_haplotype_final.g.vcf \
-V haplotypes_final/JKS2171_haplotype_final.g.vcf \
-V haplotypes_final/JKS2176_haplotype_final.g.vcf \
-V haplotypes_final/JKS2178_haplotype_final.g.vcf \
-V haplotypes_final/JKS2179_haplotype_final.g.vcf \
-V haplotypes_final/JKS2181_haplotype_final.g.vcf \
-V haplotypes_final/JKS2185_haplotype_final.g.vcf \
-V haplotypes_final/JKS2190_haplotype_final.g.vcf \
-V haplotypes_final/JKS2195_haplotype_final.g.vcf \
-V haplotypes_final/JKS2264_haplotype_final.g.vcf \
-V haplotypes_final/JKS2265_haplotype_final.g.vcf \
-V haplotypes_final/JKS2266_haplotype_final.g.vcf \
-V haplotypes_final/JKS2337_haplotype_final.g.vcf \
-V haplotypes_final/JKS2342_haplotype_final.g.vcf \
-V haplotypes_final/JKS2343_haplotype_final.g.vcf \
-V haplotypes_final/JKS2350_haplotype_final.g.vcf \
-V haplotypes_final/JKS2353_haplotype_final.g.vcf \
-V haplotypes_final/JKS2359_haplotype_final.g.vcf \
-V haplotypes_final/JKS2372_haplotype_final.g.vcf \
-V haplotypes_final/JKS2373_haplotype_final.g.vcf \
-V haplotypes_final/JKS2376_haplotype_final.g.vcf \
-V haplotypes_final/JKS2383_haplotype_final.g.vcf \
-V haplotypes_final/JKS2385_haplotype_final.g.vcf \
-V haplotypes_final/JKS2386_haplotype_final.g.vcf \
-V haplotypes_final/JKS2390_haplotype_final.g.vcf \
-V haplotypes_final/JKS2392_haplotype_final.g.vcf \
-V haplotypes_final/JKS2394_haplotype_final.g.vcf \
-V haplotypes_final/JKS2395_haplotype_final.g.vcf \
-V haplotypes_final/JKS2397_haplotype_final.g.vcf \
-V haplotypes_final/JKS2449_haplotype_final.g.vcf \
-V haplotypes_final/JKS2450_haplotype_final.g.vcf \
-V haplotypes_final/JKS2453_haplotype_final.g.vcf \
-V haplotypes_final/JKS2456_haplotype_final.g.vcf \
-V haplotypes_final/JKS2457_haplotype_final.g.vcf \
-V haplotypes_final/JKS2459_haplotype_final.g.vcf \
-V haplotypes_final/JKS2469_haplotype_final.g.vcf \
-V haplotypes_final/JKS2479_haplotype_final.g.vcf \
-V haplotypes_final/JKS2488_haplotype_final.g.vcf \
-V haplotypes_final/JKS2492_haplotype_final.g.vcf \
-V haplotypes_final/JKS2495_haplotype_final.g.vcf \
-V haplotypes_final/JKS2507_haplotype_final.g.vcf \
-V haplotypes_final/JKS2530_haplotype_final.g.vcf \
-V haplotypes_final/JKS2541_haplotype_final.g.vcf \
-V haplotypes_final/JKS2548_haplotype_final.g.vcf \
-V haplotypes_final/JKS2551_haplotype_final.g.vcf \
-V haplotypes_final/JKS2552_haplotype_final.g.vcf \
-O haplotypes_final/Pseudonocardia_paper_3_combined.g.vcf

Answers

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