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We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
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.