跑ModelSegments时输出没有结果并报错Exception in thread "main" java.lang.OutOfMemoryError: Java heap space: failed reallocation of scalar replaced objects;解决方法将--java-options "-Xmx20g"中内存调大,比如到-Xmx180g即可解决问题;
id="test"
gatk --java-options "-Xmx180g" ModelSegments --denoised-copy-ratios ./8.cnv/gatk/denoisedCR/${id}.clean.denoisedCR.tsv --allelic-counts ./8.cnv/gatk/allelicCounts/${id}.allelicCounts.tsv --normal-allelic-counts ./8.cnv/gatk/allelicCounts/${germline}.allelicCounts.tsv --output-prefix $id --output ./8.cnv/gatk/segments
参考https://github.com/broadinstitute/pilon/issues/44