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Missing chr in gVCF
I have generated a gVCF file using GATK-3.7 and it is completed without any error. However, i notice only few chromosome names in the first column of the gVCF file:
java -Xmx10G -GenomeAnalysisTK.jar -R species.fa -T HaplotypeCaller -I Input.bam -stand_call_conf 30 -ERC GVCF --min_base_quality_score 20 --variant_index_parameter 128000 --variant_index_type LINEAR --genotyping_mode DISCOVERY -o GATK.g.vcf.gz less GATK.g.vcf.gz | grep -v "##" | cut -f1| sort | uniq chr1 chr10 chr11 chr12 chr13 #CHROM
Does it mean that the run is incomplete? or ami i missing some property of gVCF format.