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Does CombineGVCFs work for haploid genomes
I have been trying to use CombinegVCFs on gVCF file produce by HaplotypeCaller in GVCF mode. The output VCF file doesn't seem to have any data in the genotype field: (just a dot)
chr1 95849 . T . . END=95850 GT:DP:GQ:MIN_DP:PL .:48:89:47:0,90 .:100:99:3:0,106
chr1 95851 . T . . END=95856 GT:DP:GQ:MIN_DP:PL .:48:44:47:0,45 .:100:99:3:0,106
chr1 95857 . GAA G,GA, . . DP=50;MQ=60.23;MQ0=0 GT:AD:DP:MIN_DP:PL:SB .:0,6,41,0:47:.:1150,935,0,1090:0,0,18,23 .:.:100:3:0,106,106,106
chr1 95858 . A . . END=95859 GT:DP:GQ:MIN_DP:PL . .:100:99:3:0,106
chr1 95860 . A . . END=96535 GT:DP:GQ:MIN_DP:PL .:44:99:27:0,1038 .:100:99:3:0,106
chr1 96536 . A G, . . DP=95;MQ=57.24;MQ0=0 GT:AD:DP:MIN_DP:PL:SB .:0,25,0:25:.:792,0,792:0,0,13,12 .:.:70:70:0,0,0
chr1 96537 . G . . END=96823 GT:DP:GQ:MIN_DP:PL .:37:99:23:0,380 .:68:99:51:0,374
chr1 96824 . C . . . GT:DP:GQ:MIN_DP:PL .:31:25:31:0,26 .:51:57:51:0,58
This is the command I used:
java -Xmx45g -Djava.io.tmpdir=/home/LANPARK/mboursnell/javatempdir -jar /opt/gatk/GenomeAnalysisTK.jar -R /home/genetics/strep_equi/strep_equi.fasta -T CombineGVCFs -V 17-1-2-5_NL_S12_L001_R1_001.gVCF -V 17-1-2-6_NL_S9_L001_R1_001.gVCF -o combined_1a.vcf -S STRICT