WES分析9-过滤&注释

过滤&注释

wkd=/home/lzn/WES
ref=/home/lzn/WES/genome/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta

gatk FilterMutectCalls \
-R $ref\
-V $wkd/mutect/GSM2653854.vcf \
-O $wkd/mutect/GSM2653854.filtered.vcf

#A USER ERROR has occurred: Mutect stats table GSM2653854.vcf.stats not found.  When Mutect2 outputs a file calls.vcf it also creates a calls.vcf.stats file.  Perhaps this file was not moved along with the vcf, or perhaps it was not delocalized from a virtual machine while running in the cloud.
#mutect2步骤没有creates a calls.vcf.stats file.
#回看日志信息，发现Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
#修改mutect2步骤代码，添加 --java-options "-Xmx16G -Djava.io.tmpdir=./"  
#依旧没有生成 calls.vcf.stats file.  垃圾软件。毁我青春。
# https://www.ershicimi.com/p/de113552755ea9d79c22ca7e78a2f3d0 别人也同样无解。