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Why I got chaotic results when I did snp calling for all-sites used by gatk22.214.171.124?
The version I used is gatk126.96.36.199.
The shell script I used is:
software/gatk-188.8.131.52/gatk --java-options "-Xmx4g" HaplotypeCaller -R NewChr.fasta -I split.bam -ERC BP_RESOLUTION -O ss.vcf
I got the some results when I used "HaplotypeCaller's -ERC BP_RESOLUTION "
NewChr1 807256 . T . PASS . GT:AD:DP:GQ:PL 0/0:5,0:5:15:0,15,225
NewChr1 808431 . G . PASS . GT:AD:DP:GQ:PL 0/0:7,0:7:18:0,18,270
NewChr1 809041 . A . PASS . GT:AD:DP:GQ:PL 0/0:5,0:5:15:0,15,225
NewChr1 817071 . A . PASS . GT:AD:DP:GQ:PL 0/0:1,49:50:0:0,0,0
NewChr1 820714 . G A, 136.77 PASS BaseQRankSum=-0.842;DP=5;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=18000.00 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:1,4,0:5:30:0|1:820688_CA_C:165,0,30,168,42,210:1,0,3,1
I am confused the most genotypes are "0/0" but their reads are different.(For example, "NewChr1 820714" the reads ratio is 1:49, but the genotype is "0/0")
Could you tell me what happend with this? By the way, How can I get the correct all-sites vcf?