Can you please provide
a) GATK 188.8.131.52
b) Exact GATK commands used :
gatk --java-options "-Xmx8G -XX:ParallelGCThreads=4 -Djava.io.tmpdir=java_tmp" HaplotypeCaller -R hg38.fasta -I chr2.realign.recal.bam -L chr2 -ERC GVCF -GQB 100 --pcr-indel-model NONE -D All_20180418.vcf.gz -O sample.chr2.g.vcf.gz
c) e.g. for the mixed type:
chr2 201915227 rs1394227290 T C,TAC
in this site contain two types T>C, T>TAC and both of them have a rsID, but only report one in the final vcf file.I have two questions. why not report all the corresponding rsID? and why this types are not split to two lines?
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