KiB Mem : 13191555+total, 42587552 free, 797532 used, 88530472 buff/cache
KiB Swap: 19531212+total, 19436460+free, 947508 used. 13036427+avail Mem
Since JohnMCMa had mentioned in #25 that GATK would achieve local realignment around indels before using HaplotypeCaller to call variants, I've tried to use bam files produced by GATK as bam inputs in GIREMI, while the error remained.
Could anyone give some solutions about it? Thanks very much!
Hi,
I've tried GIREMI on my SNV datasets generated by tophat2+picard+GATK+annovar pipline, while it reported
my command is
/home/yangxx/software/giremi-master/giremi -f $ref/Homo_sapiens_assembly38.fa -l $path/script/GIREMI/Severe_Early-New.GIREMI.input.txt -p 1 -o /$path/Result/GIREMI/ $path/Result/picard/PHPR0008_L8_I349-NewBatch2/Mark_duplicates.bam.
my SNV inputs are like below:
and
top
command displays of my server like below:Since JohnMCMa had mentioned in #25 that GATK would achieve local realignment around indels before using HaplotypeCaller to call variants, I've tried to use bam files produced by GATK as bam inputs in GIREMI, while the error remained.
Could anyone give some solutions about it? Thanks very much!