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Number of Snps differ between individual GVCF files and final vcf file

dhwanidhwani indiaMember
edited November 2019 in Ask the GATK team

I have total 96 gvcf file with respective number of variations

190 176 213 201 156 11 201 191 168 138 189 183 197 203 188 192 192 139 145 37 198 205 162 202 133 146 175 137 157 198 162 174 204 109 200 179 199 107 175 147 145 186 179 199 395 141 177 186 137 197 192 188 178 180 161 162 199 154 179 200 148 159 133 200 206 181 212 205 201 144 157 180 191 143 198 142 212 319 184 176 173 154 203 186 173 143 176 156 239 198 177 201 209 132 192 154

while the final vcf file has 166 number of variations.

The command used for GCVF generation was :java -jar ${base_path}/softwares/GenomeAnalysisTK.jar -T HaplotypeCaller -R ${base_path}/reference/${ref_file_name}.fasta -I ${base_path}/base_recalib/$i_aligned_sorted_dupmarked_realigned_recalibrated.bam --emitRefConfidence GVCF --dbsnp ${base_path}/reference/${vcf_file_name} -L ${base_path}/reference/${bed_file_name} -o ${base_path}/haplotype_caller/$i_snps.g.vcf

while the command used to make vcf was:

java -jar ${base_path}/softwares/GenomeAnalysisTK.jar -T GenotypeGVCFs -R ${base_path}/reference/${ref_file_name}.fasta --variant 76_snps.g.vcf --variant 77_snps.g.vcf --variant 78_snps.g.vcf --variant 79_snps.g.vcf --variant 80_snps.g.vcf --variant 81_snps.g.vcf --variant 82_snps.g.vcf --variant 83_snps.g.vcf --variant 84_snps.g.vcf --variant 85_snps.g.vcf --variant 86_snps.g.vcf --variant 87_snps.g.vcf --variant 88_snps.g.vcf --variant 89_snps.g.vcf --variant 90_snps.g.vcf --variant 91_snps.g.vcf ................................... --variant 70_snps.g.vcf --variant 71_snps.g.vcf -ploidy 2 -o output.vcf

**DOES GenotypeGVCFs combine only those variations to VCF that have alternate alleles? How do we account for reduction of SNPs in VCF file. Is there any way to preserve all the positions present in GVCF file **

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