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Can I disable local reassembly and realignment?
I want to dentify short variants in RNAseq data. But I find HaplotypeCaller introduces many unusual alignments (see the raw bam and bamout file).
Can I disable local reassembly and realignment or any ways to solve this problem?
My GATK version is 126.96.36.199.
My commands are:
gatk SplitNCigarReads -R ref.fa -I STAR.mapped.remove_dup.bam -O SplitN.bam
gatk HaplotypeCaller -R ref.fa -I SplitN.bam -O output.g.vcf.gz -ERC GVCF -bamout bamout.bam