c) Why do I see (......)?
I'm using GATK v18.104.22.168 to call variants from short reads with Haplotypecaller.
In the gvcf and vcf resulting from the command line, a variant is called with a high number of alternative alleles :
chr17 78064001 . G A 469.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.082;DP=368;ExcessHet=3.0103;FS=81.951;MLEAC=1;MLEAF=0.500;MQ=55.41;MQRankSum=1.060;QD=2.45;ReadPosRankSum=8.442;SOR=3.353 GT:AD:DP:GQ:PL 0/1:106,86:192:99:477,0,2190
When I look in the initial bam used to do the calling, I can't see more than 4 alt alleles on several at this position, neither in the bam resultig from the HaplotyCaller bammout command.
How is it possible ? It seems to be a calling error for me.
Here is the command line :
/GATK/gatk-4/gatk HaplotypeCaller -R /public-data/genome/HG19/fasta/all.fa -I /initial.bam --output resulting.gvcf --output-mode EMIT_ALL_CONFIDENT_SITES -bamout realigned.bam --java-options '-Xmx40G -Xms40g'
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